Agilent Gene Expression Microarray Report

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Customer Institutaion	XXXXXXX
Customer Email	XXXXXXX
Project ID	XXXXXXX

Salesperson	Kyle Navel
Email	knavel@lcsciences.com

Your reliable partner in genomics, transcriptomics and proteomics

LC Sciences

1. Project information

1.1 Sample information

Species name: Human

Latin name: Homo sapiens

Specimens: tissue

1.2 Group information

SampleID	species	cond1
Control_1	hsa	Control
Control_2	hsa	Control
Control_3	hsa	Control
Treatment_1	hsa	Treatment
Treatment_2	hsa	Treatment
Treatment_3	hsa	Treatment

1.3 Database

Dababase	Web links	Version/date
Gene Orthology (GO)	https://www.ncbi.nlm.nih.gov/projects/SNP/	2016.12
KEGG	http://www.kegg.jp/	2017.06

1.4 Bioinformatics software

Analysis item	Software	Version/date
Data normalization	Genespring	14.8
GO and KEGG enrichment analysis	Perl scripts in house	NA
Drawing tools	R,cytoacape	3.3.0,3.5.1

LC Sciences

2. Materials and Methods

2.1 Experimental methods

Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G5761A (Agilent Technologies).

2.2 Bioinformatics analysis

Feature Extraction software (version12.0.3.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version14.8, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0, or pvalue<=0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNA. Finally, Hierarchical Clustering was performed to display the distinguishable genes'expression pattern among samples.

Bioinformatics pipeline for mRNA microarray

LC Sciences

3. Results

3.1 Data normalization

Importing raw data into Genespring software (version14.8, Agilent), using quantile method to standardize data, including normalized signal values, sample detection and detailed annotation information.

ProbeName

Control_1_NormSignal

Control_2_NormSignal

Control_3_NormSignal

Treatment_1_NormSignal

Treatment_2_NormSignal

Treatment_3_NormSignal

Treatment_3_flags

Control_3_flags

Treatment_2_flags

Control_1_flags

Treatment_1_flags

Control_2_flags

PrimaryAccession

RefSeqAccession

GenbankAccession

UniGeneID

EntrezGeneID

GeneSymbol

GeneName

EnsemblID

Description

chr

start

end

GE_BrightCorner

18.50

18.35

18.23

18.37

18.36

18.13

Detected

DarkCorner

3.53

3.34

3.95

3.44

3.29

3.48

Not Detected

A_21_P0014386

6.25

6.90

7.24

7.47

6.57

7.05

Detected

Not Detected

Detected

A_33_P3396872

8.26

8.66

7.93

8.89

8.86

9.00

Detected

ref|NM_001105533|gb|AK025639|gb|BC030538|tc|THC2601673

NM_001105533

Hs.189652

79974

CPED1

cadherin-like and PC-esterase domain containing 1

Homo sapiens cadherin-like and PC-esterase domain containing 1 (CPED1), transcript variant 2, mRNA [NM_001105533]

chr7

120901888

120901947

A_33_P3267760

9.39

9.86

9.29

9.30

9.45

10.38

Detected

ens|ENST00000378463

54880

BCOR

BCL6 corepressor

ENST00000378463

BCL6 corepressor [Source:HGNC Symbol;Acc:HGNC:20893] [ENST00000378463]

chrX

39909128

39909069

A_32_P194264

10.14

11.98

11.74

10.24

11.31

10.00

Detected

ref|NM_001008708|ens|ENST00000295304|gb|HQ447717|gb|BC017941

NM_001008708

Hs.585944

494143

CHAC2

ChaC, cation transport regulator homolog 2 (E. coli)

ENST00000295304

Homo sapiens ChaC, cation transport regulator homolog 2 (E. coli) (CHAC2), mRNA [NM_001008708]

chr2

54001454

54001513

A_23_P153745

10.99

12.22

10.13

11.28

11.04

11.74

Detected

ref|NM_006332|ens|ENST00000593731|ens|ENST00000600463|ens|ENST00000407280

NM_006332

Hs.14623

10437

IFI30

interferon, gamma-inducible protein 30

ENST00000593731

Homo sapiens interferon, gamma-inducible protein 30 (IFI30), mRNA [NM_006332]

chr19

18288840

18288899

A_33_P3352837

9.79

9.35

9.41

9.47

9.64

Detected

chr2

171521262

171521203

A_21_P0011260

5.53

7.14

7.00

5.45

6.48

6.82

Detected

Not Detected

Detected

ens|ENST00000618272|linc|TCONS_l2_00007928|gb|BI821606|tc|THC2662262

Hs.592320

ENST00000618272

603036639F1 NIH_MGC_115 Homo sapiens cDNA clone IMAGE:5177672 5', mRNA sequence [BI821606]

chr14

103675125

103675184

A_33_P3235816

3.92

4.31

3.93

3.63

3.26

3.53

Not Detected

ens|ENST00000436258|gb|BX647611|tc|THC2646539

BX647611

Hs.594815

ENST00000436258

DPY19L2 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:22305] [ENST00000436258]

chr7

35129516

35129457

A_21_P0014180

9.55

9.86

10.20

9.56

9.75

10.53

Detected

ens|ENST00000474396|tc|THC2637218

XM_006715643

115330

GPR146

G protein-coupled receptor 146

ENST00000474396

G protein-coupled receptor 146 [Source:HGNC Symbol;Acc:HGNC:21718] [ENST00000474396]

chr7

1095841

1095900

A_24_P944991

9.69

10.76

10.68

9.97

10.00

10.36

Detected

ref|NM_173829|ens|ENST00000513458|gb|BC127085|gb|BC127086

NM_173829

Hs.69504

285672

SREK1IP1

SREK1-interacting protein 1

ENST00000513458

Homo sapiens SREK1-interacting protein 1 (SREK1IP1), mRNA [NM_173829]

chr5

64018946

64018887

A_21_P0006507

3.89

5.22

4.80

6.09

4.70

5.51

Not Detected

Detected

Not Detected

linc|lnc-ARMCX4-1:1|linc|TCONS_00017209

lnc-ARMCX4-1

lnc-ARMCX4-1:1

LNCipedia lincRNA (lnc-ARMCX4-1), lincRNA [lnc-ARMCX4-1:1]

chrX

100672726

100672785

A_23_P208706

11.13

11.84

11.71

11.33

11.73

11.56

Detected

ref|NM_138764|ref|NM_001291428|ref|NM_001291431|ref|NM_138761

NM_138764

Hs.624291

581

BAX

BCL2-associated X protein

ENST00000513545

Homo sapiens BCL2-associated X protein (BAX), transcript variant sigma, mRNA [NM_138764]

chr19

49464904

49464963

A_33_P3388806

4.19

3.44

3.63

3.61

4.38

3.47

Not Detected

ref|NM_001199327|gb|BC032865|ens|ENST00000370899|tc|THC2476487

NM_001199327

Hs.480085

100526835

FPGT-TNNI3K

FPGT-TNNI3K readthrough

ENST00000370899

Homo sapiens FPGT-TNNI3K readthrough (FPGT-TNNI3K), transcript variant 2, mRNA [NM_001199327]

chr1

74930515

74930574

A_33_P3324839

11.32

11.22

11.42

11.81

11.33

11.71

Detected

ref|NM_006772|ens|ENST00000418600|ens|ENST00000455687|gb|AL713634

NM_006772

Hs.586264

8831

SYNGAP1

synaptic Ras GTPase activating protein 1

ENST00000418600

Homo sapiens synaptic Ras GTPase activating protein 1 (SYNGAP1), mRNA [NM_006772]

chr6

33420559

33420618

A_24_P333494

9.54

10.95

10.84

10.39

10.76

10.82

Detected

ref|NM_018994|ens|ENST00000375592|ref|XM_006710698|gb|BC006174

NM_018994

Hs.522384

54455

FBXO42

F-box protein 42

ENST00000375592

Homo sapiens F-box protein 42 (FBXO42), mRNA [NM_018994]

chr1

16577198

16577139

A_22_P00006274

7.65

7.41

7.76

7.84

6.98

8.85

Detected

ref|NR_109772|ens|ENST00000413050|ens|ENST00000437181|linc|lnc-FAM75D1-1:3

NR_109772

Hs.528628

101927502

LOC101927502

uncharacterized LOC101927502

ENST00000413050

Homo sapiens uncharacterized LOC101927502 (LOC101927502), long non-coding RNA [NR_109772]

chr9

84362930

84362989

A_23_P161615

12.28

12.86

12.98

11.72

11.96

11.47

Detected

ens|ENST00000534785|ens|ENST00000527618|ens|ENST00000527850|gb|AK307831

AK307831

Hs.201897

23649

POLA2

polymerase (DNA directed), alpha 2, accessory subunit

ENST00000534785

polymerase (DNA directed), alpha 2, accessory subunit [Source:HGNC Symbol;Acc:HGNC:30073] [ENST00000534785]

chr11

65062111

65063057

A_33_P3384958

9.46

9.23

9.43

9.47

9.49

9.36

Detected

ref|NM_014839|ref|NM_001166252|ens|ENST00000457765|ens|ENST00000370185

NM_014839

Hs.13245

9890

LPPR4

lipid phosphate phosphatase-related protein type 4

ENST00000457765

Homo sapiens lipid phosphate phosphatase-related protein type 4 (LPPR4), transcript variant 1, mRNA [NM_014839]

chr1

99771632

99771691

A_22_P00018955

6.54

5.82

5.33

4.79

4.34

5.27

Not Detected

Detected

Not Detected

Detected

linc|lnc-SOX11-1:1|gb|BX089860|tc|THC2729651

BX089860

Hs.597532

lnc-SOX11-1

lnc-SOX11-1:1

BX089860 NCI_CGAP_Brn23 Homo sapiens cDNA clone IMAGp998P014327 ; IMAGE:1704048, mRNA sequence [BX089860]

chr2

5847732

5847791

A_22_P00009547

6.45

3.39

3.52

3.57

3.27

3.39

Not Detected

Detected

Not Detected

ref|NR_126414|linc|lnc-MAP2K6-3:1|gb|CB960713|tc|THC2717445

NR_126414

Hs.569827

104355297

ABCA9-AS1

ABCA9 antisense RNA 1

Homo sapiens ABCA9 antisense RNA 1 (ABCA9-AS1), long non-coding RNA [NR_126414]

chr17

67008185

67008244

A_23_P218331

10.53

11.45

10.88

11.70

11.30

11.95

Detected

ref|NM_001017916|ref|NM_001017917|ref|NM_001915|ens|ENST00000581573

NM_001017916

Hs.355264

1534

CYB561

cytochrome b561

ENST00000581573

Homo sapiens cytochrome b561 (CYB561), transcript variant 2, mRNA [NM_001017916]

chr17

61510687

61510628

A_33_P6455786

13.90

14.30

14.26

14.60

14.49

14.32

Detected

ref|NM_058172|ref|NM_001286781|ref|NM_001286780|ens|ENST00000403729

NM_058172

Hs.162963

118429

ANTXR2

anthrax toxin receptor 2

ENST00000403729

Homo sapiens anthrax toxin receptor 2 (ANTXR2), transcript variant 1, mRNA [NM_058172]

chr4

80822879

80822820

A_21_P0008705

8.68

8.20

8.84

9.02

8.93

8.84

Detected

lnc-POTEB-5

lnc-POTEB-5:4

LNCipedia lincRNA (lnc-POTEB-5), lincRNA [lnc-POTEB-5:4]

chr15

22541615

22541556

A_22_P00016526

3.73

3.36

3.47

3.55

3.27

3.35

Not Detected

Hs.148998

ENST00000547094

chr12

90343407

90343466

A_33_P3235207

3.72

4.50

3.45

4.23

5.52

3.34

Not Detected

Detected

Not Detected

ref|NM_018018|ref|NM_001143824|ens|ENST00000547477|ens|ENST00000266579

NM_018018

Hs.446077

55089

SLC38A4

solute carrier family 38, member 4

ENST00000547477

Homo sapiens solute carrier family 38, member 4 (SLC38A4), transcript variant 1, mRNA [NM_018018]

chr12

47173627

47173568

A_33_P3330991

15.13

14.72

14.47

14.69

14.53

14.87

Detected

ref|XR_248772|gb|AK128451|tc|NP850545

XR_248772

Hs.199368

100134237

LOC100134237

uncharacterized LOC100134237

PREDICTED: Homo sapiens uncharacterized LOC100134237 (LOC100134237), misc_RNA [XR_248772]

chr1

32012152

32012211

A_33_P3374299

9.43

9.01

9.12

9.47

9.28

10.14

Detected

ref|NM_173561|ens|ENST00000373164|ens|ENST00000470102|ens|ENST00000244565

NM_173561

Hs.158357

222643

UNC5CL

unc-5 homolog C (C. elegans)-like

ENST00000373164

Homo sapiens unc-5 homolog C (C. elegans)-like (UNC5CL), mRNA [NM_173561]

chr6

40998222

40998163

A_33_P3274701

14.05

13.37

13.34

13.53

14.75

13.17

Detected

gb|AK024162|tc|THC2483964

AK024162

Homo sapiens cDNA FLJ14100 fis, clone MAMMA1000855. [AK024162]

chr1

2144562

2144503

A_23_P83436

10.45

10.43

10.68

11.32

10.55

11.21

Detected

ref|NM_000285|ref|NM_001166056|ref|NM_001166057|ens|ENST00000591968

NM_000285

Hs.36473

5184

PEPD

peptidase D

ENST00000591968

Homo sapiens peptidase D (PEPD), transcript variant 1, mRNA [NM_000285]

chr19

33877995

33877936

A_33_P3243138

8.49

8.76

9.01

8.42

9.03

8.56

Detected

ref|NM_182704|ens|ENST00000600586|ens|ENST00000335426|ens|ENST00000622070

NM_182704

Hs.319284

348303

SELV

selenoprotein V

ENST00000600586

Homo sapiens selenoprotein V (SELV), mRNA [NM_182704]

chr19

40009729

40009788

A_22_P00008018

5.74

5.45

5.60

5.76

6.39

6.46

Detected

Not Detected

Detected

Not Detected

ens|ENST00000579045|linc|lnc-IFT20-3:1|gb|BC082966|tc|THC2513242

BC082966

Hs.20588

ENST00000579045

Homo sapiens cDNA clone IMAGE:6341252. [BC082966]

chr17

26574222

26574163

A_22_P00003937

3.63

3.33

3.36

3.49

3.26

3.28

Not Detected

ens|ENST00000569945|linc|lnc-CGNL1-1:1|gb|BX641062|tc|THC2709601

BX641062

Hs.711270

145781

GCOM1

GRINL1A complex locus 1

ENST00000569945

GRINL1A complex locus 1 [Source:HGNC Symbol;Acc:HGNC:26424] [ENST00000569945]

chr15

57984823

57984882

ERCC-00109_120

6.98

7.22

6.81

7.32

7.04

7.70

Detected

DQ854998

A_33_P3293593

8.07

7.96

7.98

8.57

7.49

8.06

Detected

ref|NM_152479|ens|ENST00000311308|ens|ENST00000593586|gb|BC029539

NM_152479

Hs.631572

148014

TTC9B

tetratricopeptide repeat domain 9B

ENST00000311308

Homo sapiens tetratricopeptide repeat domain 9B (TTC9B), mRNA [NM_152479]

chr19

40722025

40721966

A_22_P00008389

3.99

3.97

6.00

4.81

5.66

5.55

Not Detected

Detected

Not Detected

ref|NM_001145545|ens|ENST00000505035|ens|ENST00000418886|linc|lnc-JMJD5-1:1

NM_001145545

Hs.120831

162083

C16orf82

chromosome 16 open reading frame 82

ENST00000505035

Homo sapiens chromosome 16 open reading frame 82 (C16orf82), mRNA [NM_001145545]

chr16

27080048

27080107

A_21_P0012208

6.55

9.30

9.03

7.27

8.37

7.60

Detected

Hs.596577

lnc-C21orf58-1

lnc-C21orf58-1:1

Homo sapiens cDNA FLJ45665 fis, clone CTONG2027959. [AK127572]

chr21

47875234

47875175

A_23_P101084

7.48

6.95

7.01

6.70

7.38

7.07

Detected

ref|NM_032598|ref|NM_001170698|ref|NM_001170697|ref|NM_001170695

NM_032598

Hs.351068

84690

SPATA22

spermatogenesis associated 22

ENST00000573128

Homo sapiens spermatogenesis associated 22 (SPATA22), transcript variant 2, mRNA [NM_032598]

chr17

3346555

3346496

A_23_P162120

13.60

14.00

13.51

13.56

13.61

13.42

Detected

ref|NM_006185|ref|NM_001286561|ref|NR_104476|ens|ENST00000616538

NM_006185

Hs.325978

4926

NUMA1

nuclear mitotic apparatus protein 1

ENST00000616538

Homo sapiens nuclear mitotic apparatus protein 1 (NUMA1), transcript variant 1, mRNA [NM_006185]

chr11

71715302

71715118

A_24_P291426

10.19

10.66

10.79

10.68

10.30

10.49

Detected

ref|NM_016316|ref|NM_001037872|ens|ENST00000258428|ens|ENST00000393445

NM_016316

Hs.443077

51455

REV1

REV1, polymerase (DNA directed)

ENST00000258428

Homo sapiens REV1, polymerase (DNA directed) (REV1), transcript variant 1, mRNA [NM_016316]

chr2

100019124

100018768

A_32_P99311

6.03

6.97

6.26

7.64

7.18

6.18

Detected

ref|NM_181756|ref|NM_001207005|ens|ENST00000391958|gb|AK055310

NM_181756

Hs.466891

353355

ZNF233

zinc finger protein 233

ENST00000391958

Homo sapiens zinc finger protein 233 (ZNF233), transcript variant 1, mRNA [NM_181756]

chr19

44779060

44779119

A_21_P0011409

6.98

8.69

8.19

8.09

8.08

8.66

Detected

linc|TCONS_l2_00009502|gb|AK125393|tc|THC2508977

Hs.586876

XLOC_l2_004898

BROAD Institute lincRNA (XLOC_l2_004898), lincRNA [TCONS_l2_00009502]

chr15

40983434

40983375

A_24_P198629

9.39

9.68

9.36

9.73

9.45

10.15

Detected

ref|NM_001040616|ens|ENST00000559169|ref|XM_005254941|ref|XM_005254943

NM_001040616

Hs.105633

55180

LINS

lines homolog (Drosophila)

ENST00000559169

Homo sapiens lines homolog (Drosophila) (LINS), mRNA [NM_001040616]

chr15

101109837

101109778

A_19_P00322925

9.59

9.12

9.01

9.47

9.93

9.94

Detected

Hs.188825

ENST00000607519

GMDS antisense RNA 1 (head to head) [Source:HGNC Symbol;Acc:HGNC:48993] [ENST00000607519]

chr6

2481189

2481248

A_22_P00025188

5.26

3.88

3.27

6.10

4.98

5.05

Not Detected

Detected

Not Detected

ENST00000512831

Q6NT14_HUMAN (Q6NT14) ZNF80 protein (Fragment), partial (13%) [THC2642096]

chr4

163662989

163663048

A_23_P52610

10.77

11.07

11.06

10.00

9.55

9.54

Detected

ref|NM_000107|ref|NM_001300734|ens|ENST00000378601|ens|ENST00000617847

NM_000107

Hs.700338

1643

DDB2

damage-specific DNA binding protein 2, 48kDa

ENST00000378601

Homo sapiens damage-specific DNA binding protein 2, 48kDa (DDB2), mRNA [NM_000107]

chr11

47260623

47260682

A_22_P00004622

3.49

4.65

5.30

4.99

3.45

4.60

Not Detected

linc|lnc-CST7-2:1

lnc-CST7-2

lnc-CST7-2:1

LNCipedia lincRNA (lnc-CST7-2), lincRNA [lnc-CST7-2:1]

chr20

24998440

24998499

A_23_P2814

10.49

10.13

9.90

10.93

9.77

10.55

Detected

ref|NM_005905|ref|NM_001127217|ens|ENST00000379826|ens|ENST00000350148

NM_005905

Hs.123119

4093

SMAD9

SMAD family member 9

ENST00000379826

Homo sapiens SMAD family member 9 (SMAD9), transcript variant b, mRNA [NM_005905]

chr13

37422872

37422813

A_23_P140602

12.90

13.49

12.85

13.17

13.11

13.29

Detected

ref|NM_001033088|ref|NR_028052|ens|ENST00000561573|gb|AK312641

NM_001033088

Hs.135471

51335

NGRN

neugrin, neurite outgrowth associated

ENST00000561573

Homo sapiens neugrin, neurite outgrowth associated (NGRN), transcript variant 2, mRNA [NM_001033088]

chr15

90814473

90814532

A_33_P3276112

12.92

12.79

12.19

12.47

13.59

11.70

Detected

linc|lnc-CTD-2517M22.14.1-1:3|linc|lnc-CTD-2517M22.14.1-1:4|gb|AK126743|tc|THC2487449

AK126743

Hs.521937

lnc-CTD-2517M22.14.1-1

lnc-CTD-2517M22.14.1-1:3

Homo sapiens cDNA FLJ44789 fis, clone BRACE3038760. [AK126743]

chr8

145722802

145722743

A_21_P0012896

7.80

7.77

9.10

8.13

8.44

7.96

Detected

linc|TCONS_l2_00022830|tc|THC2775530

XLOC_l2_011987

BROAD Institute lincRNA (XLOC_l2_011987), lincRNA [TCONS_l2_00022830]

chr5

34124290

34124231

A_22_P00010379

7.62

8.01

8.47

7.50

8.03

8.11

Detected

linc|lnc-MYL12A-1:1|gb|AK093324|tc|THC2533948

AK093324

Hs.589563

lnc-MYL12A-1

lnc-MYL12A-1:1

Homo sapiens cDNA FLJ36005 fis, clone TESTI2015350. [AK093324]

chr18

3247111

3247170

A_23_P210939

13.51

15.04

14.51

14.56

14.45

14.64

Detected

ref|NM_181468|ref|NM_002212|ref|NM_181466|ref|NM_001267810

NM_181468

Hs.743992

3692

EIF6

eukaryotic translation initiation factor 6

ENST00000374450

Homo sapiens eukaryotic translation initiation factor 6 (EIF6), transcript variant 2, mRNA [NM_181468]

chr20

33866998

33866939

A_24_P349039

8.67

10.61

10.31

9.09

10.26

9.63

Detected

ref|NM_020754|ens|ENST00000264245|ref|XM_006713714|ref|XM_005247671

NM_020754

Hs.668218

57514

ARHGAP31

Rho GTPase activating protein 31

ENST00000264245

Homo sapiens Rho GTPase activating protein 31 (ARHGAP31), mRNA [NM_020754]

chr3

119136009

119136068

A_24_P143686

11.41

12.48

12.78

12.35

11.87

11.94

Detected

ref|NM_001080394|ref|NM_001282919|ref|NM_001282916|ref|NR_104581

NM_001080394

Hs.381058

23514

SPIDR

scaffolding protein involved in DNA repair

ENST00000297423

Homo sapiens scaffolding protein involved in DNA repair (SPIDR), transcript variant 1, mRNA [NM_001080394]

chr8

48642027

48647927

A_23_P115346

12.06

12.25

12.52

11.93

11.07

11.77

Detected

ref|NM_006893|ref|NM_001201478|ens|ENST00000468891|ens|ENST00000484492

NM_006893

Hs.497581

1939

EIF2D

eukaryotic translation initiation factor 2D

ENST00000468891

Homo sapiens eukaryotic translation initiation factor 2D (EIF2D), transcript variant 1, mRNA [NM_006893]

chr1

206770531

206770472

A_22_P00010590

6.58

3.23

4.98

5.13

4.07

3.99

Not Detected

Detected

Not Detected

ens|ENST00000553534|linc|lnc-NDRG2-3:1

ENST00000553534

chr14

21404323

21404264

A_22_P00014892

16.17

15.70

15.85

16.19

15.65

Detected

BC038731

Hs.561806

ENST00000521326

Homo sapiens cDNA clone IMAGE:5267578. [BC038731]

chr8

87355370

87355311

A_21_P0014148

3.36

3.23

3.20

3.30

3.21

3.15

Not Detected

gb|XR_108599

XR_108599

Hs.570950

PREDICTED: Homo sapiens uncharacterized LOC100506329 (LOC100506329), misc_RNA [XR_108599]

chr5

50757933

50757992

A_21_P0012259

11.51

11.72

11.88

11.09

12.97

10.38

Detected

Compromised

Detected

linc|TCONS_l2_00017650|linc|TCONS_l2_00017653

XLOC_l2_009328

BROAD Institute lincRNA (XLOC_l2_009328), lincRNA [TCONS_l2_00017650]

chr22

24663001

24663060

A_33_P3237393

3.35

3.22

3.19

3.29

3.20

3.14

Not Detected

ref|NM_001300778|ref|NM_003440|ref|NM_001300777|ref|NM_001300776

NM_001300778

Hs.181552

7699

ZNF140

zinc finger protein 140

Homo sapiens zinc finger protein 140 (ZNF140), transcript variant 4, mRNA [NM_001300778]

chr12

133684178

133684237

A_23_P251486

6.93

7.30

6.61

6.57

6.47

6.79

Detected

ref|NM_006438|gb|AB002631|tc|THC2478678

NM_006438

Hs.176615

10584

COLEC10

collectin sub-family member 10 (C-type lectin)

Homo sapiens collectin sub-family member 10 (C-type lectin) (COLEC10), mRNA [NM_006438]

chr8

120118876

120118935

A_33_P3227880

7.91

8.14

8.01

8.40

6.76

8.23

Detected

ref|NM_001197247|ref|NM_001145009|ens|ENST00000396948|ens|ENST00000425234

NM_001197247

Hs.376046

11118

BTN3A2

butyrophilin, subfamily 3, member A2

ENST00000396948

Homo sapiens butyrophilin, subfamily 3, member A2 (BTN3A2), transcript variant 3, mRNA [NM_001197247]

chr6

26375985

26376044

A_33_P3267305

11.42

12.06

11.77

11.94

11.27

12.00

Detected

ref|NM_173595|ens|ENST00000267116|ens|ENST00000548241|gb|AK056831

NM_173595

Hs.524506

283373

ANKRD52

ankyrin repeat domain 52

ENST00000267116

Homo sapiens ankyrin repeat domain 52 (ANKRD52), mRNA [NM_173595]

chr12

56631650

56631591

A_22_P00017513

3.87

6.42

5.66

5.77

5.07

5.42

Not Detected

Detected

linc|lnc-WDFY2-1:1|tc|THC2661765|tc|THC2604700

lnc-WDFY2-1

lnc-WDFY2-1:1

Q9BSH2_HUMAN (Q9BSH2) MARVELD3 protein (Fragment), partial (10%) [THC2604700]

chr13

52378813

52378872

A_21_P0005768

4.93

5.36

6.49

3.29

3.62

3.13

Not Detected

Detected

Not Detected

NR_126028

552853

NCRNA00250

non-protein coding RNA 250

ENST00000519500

Homo sapiens non-protein coding RNA 250 (NCRNA00250), long non-coding RNA [NR_126028]

chr8

135854504

135854698

A_21_P0013237

9.52

8.86

8.90

9.40

9.31

9.09

Detected

linc|lnc-VKORC1L1-2:1|linc|TCONS_l2_00025988

lnc-VKORC1L1-2

lnc-VKORC1L1-2:1

LNCipedia lincRNA (lnc-VKORC1L1-2), lincRNA [lnc-VKORC1L1-2:1]

chr7

66006707

66006766

A_21_P0003068

3.30

3.94

3.97

4.91

4.53

3.43

Not Detected

linc|lnc-RP11-433C9.2.1-1:2|linc|TCONS_00006330

lnc-RP11-433C9.2.1-1

lnc-RP11-433C9.2.1-1:2

LNCipedia lincRNA (lnc-RP11-433C9.2.1-1), lincRNA [lnc-RP11-433C9.2.1-1:2]

chr3

184119448

184144427

A_33_P3333642

12.41

11.71

11.51

12.11

12.71

11.32

Detected

ens|ENST00000399003|linc|lnc-MPEG1-1:1|gb|AK131315|tc|THC2487937

AK131315

Hs.533590

ENST00000399003

Homo sapiens cDNA FLJ16303 fis, clone PROST2019487. [AK131315]

chr11

59036408

59036349

A_24_P42557

3.28

3.19

3.16

3.25

3.19

3.12

Not Detected

ref|NM_001018036|ref|NM_001142626|ens|ENST00000342443|ens|ENST00000554435

NM_001018036

Hs.160411

7253

TSHR

thyroid stimulating hormone receptor

ENST00000342443

Homo sapiens thyroid stimulating hormone receptor (TSHR), transcript variant 2, mRNA [NM_001018036]

chr14

81557464

81558910

A_21_P0014207

8.59

7.70

8.41

7.12

8.76

Detected

ref|XR_242321|ref|XR_250248|ref|XR_252275|tc|THC2645710

XR_242321

101927721

LOC101927721

uncharacterized LOC101927721

PREDICTED: Homo sapiens uncharacterized LOC101927721 (LOC101927721), ncRNA [XR_242321]

chr7

100944565

100944624

A_22_P00021565

13.41

12.48

12.77

13.60

12.66

13.69

Detected

ens|ENST00000531523|linc|lnc-RNF151-1:1|tc|THC2732461

677844

SNORA78

small nucleolar RNA, H/ACA box 78

ENST00000531523

small nucleolar RNA host gene 9 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:33102] [ENST00000531523]

chr16

2015451

2015510

A_21_P0000102

17.93

17.88

18.03

18.06

17.72

18.01

Detected

ref|NM_001190470|ens|ENST00000604882

NM_001190470

Hs.666077

100462981

MTRNR2L2

MT-RNR2-like 2

ENST00000604882

Homo sapiens MT-RNR2-like 2 (MTRNR2L2), mRNA [NM_001190470]

chr5

79945878

79945819

A_24_P401090

13.01

11.09

11.22

12.39

11.37

11.78

Detected

ens|ENST00000442006

ENST00000442006

chr1

39175954

39176015

A_21_P0003288

3.26

3.17

3.14

3.23

3.18

3.11

Not Detected

ENST00000479244

chr3

86313788

86313729

A_24_P914625

10.53

10.80

11.02

10.71

10.31

10.51

Detected

ref|NM_207406|ref|NM_001159547|ens|ENST00000611697|ens|ENST00000504360

NM_207406

Hs.120591

389206

BEND4

BEN domain containing 4

ENST00000611697

Homo sapiens BEN domain containing 4 (BEND4), transcript variant 1, mRNA [NM_207406]

chr4

42145792

42145733

A_33_P3393543

5.99

6.34

6.98

6.81

6.33

5.87

Detected

gb|AL831916

AL831916

Hs.590968

400692

LOC400692

uncharacterized LOC400692

Homo sapiens mRNA; cDNA DKFZp761D1918 (from clone DKFZp761D1918). [AL831916]

chr19

38036489

38036430

A_22_P00025856

8.42

8.43

8.03

8.52

7.87

8.30

Detected

100132735

LOC100132735

uncharacterized LOC100132735

ENST00000414038

chr6

140176043

140176102

A_23_P10559

8.54

7.96

8.30

8.13

7.94

7.71

Detected

ref|NM_001080395|ref|NM_004920|ens|ENST00000374792|ens|ENST00000570932

NM_001080395

Hs.514575

9625

AATK

apoptosis-associated tyrosine kinase

ENST00000374792

Homo sapiens apoptosis-associated tyrosine kinase (AATK), transcript variant 1, mRNA [NM_001080395]

chr17

79091254

79091195

A_23_P109636

10.62

10.15

10.10

11.04

10.70

11.23

Detected

ref|NM_015541|ens|ENST00000496559|ens|ENST00000383703|ens|ENST00000273261

NM_015541

Hs.518055

26018

LRIG1

leucine-rich repeats and immunoglobulin-like domains 1

ENST00000496559

Homo sapiens leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1), mRNA [NM_015541]

chr3

66429656

66429597

A_22_P00011325

14.71

14.45

13.82

14.05

14.61

14.10

Detected

linc|lnc-OST4-2:3|linc|lnc-OST4-2:2

AK125769

Hs.666730

lnc-OST4-2

lnc-OST4-2:3

LNCipedia lincRNA (lnc-OST4-2), lincRNA [lnc-OST4-2:3]

chr2

27237428

27237369

A_22_P00000881

7.66

7.62

7.91

7.98

6.87

7.96

Detected

ref|NM_001010881|ens|ENST00000433342|linc|lnc-AGTRAP-1:1|ref|XM_006710068

NM_001010881

Hs.730573

284498

C1orf167

chromosome 1 open reading frame 167

ENST00000433342

Homo sapiens chromosome 1 open reading frame 167 (C1orf167), mRNA [NM_001010881]

chr1

11826106

11826165

A_24_P143301

10.99

11.08

10.85

11.60

11.51

12.08

Detected

ref|NM_181337|ens|ENST00000274766|gb|AF181722

NM_181337

Hs.697888

353219

KAAG1

kidney associated antigen 1

ENST00000274766

Homo sapiens kidney associated antigen 1 (KAAG1), mRNA [NM_181337]

chr6

24357605

24357664

A_22_P00010333

9.28

9.05

9.43

9.44

8.57

9.20

Detected

ENST00000452888

chr6

134957640

134957699

A_23_P215406

12.80

13.12

13.21

12.61

12.02

12.57

Detected

ref|NM_018890|ref|NM_006908|ens|ENST00000348035|gb|AK054993

NM_018890

Hs.413812

5879

RAC1

ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)

ENST00000348035

Homo sapiens ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) (RAC1), transcript variant Rac1b, mRNA [NM_018890]

chr7

6443013

6443072

A_22_P00011550

4.79

3.14

3.22

5.26

4.60

4.36

Not Detected

Hs.738310

lnc-PCDH18-1

lnc-PCDH18-1:4

LNCipedia lincRNA (lnc-PCDH18-1), lincRNA [lnc-PCDH18-1:4]

chr4

138628424

138628365

A_21_P0003096

11.20

11.65

11.29

10.37

10.79

10.23

Detected

linc|lnc-IL5RA-3:1|linc|TCONS_00006396

lnc-IL5RA-3

lnc-IL5RA-3:1

LNCipedia lincRNA (lnc-IL5RA-3), lincRNA [lnc-IL5RA-3:1]

chr3

2139272

2139213

A_21_P0013738

6.05

7.38

7.47

7.07

6.94

7.19

Detected

linc|TCONS_l2_00030040|gb|DQ673932|gb|DQ673931

XLOC_l2_015315

BROAD Institute lincRNA (XLOC_l2_015315), lincRNA [TCONS_l2_00030040]

chr9

102128039

102127202

A_21_P0010286

6.18

6.62

6.54

7.02

7.33

7.43

Detected

linc|lnc-PRDM15-1:1|linc|TCONS_00029147

lnc-PRDM15-1

lnc-PRDM15-1:1

LNCipedia lincRNA (lnc-PRDM15-1), lincRNA [lnc-PRDM15-1:1]

chr21

43209077

43209018

A_24_P336113

10.84

10.90

10.91

10.67

10.79

10.66

Detected

ref|NM_012295|ref|NM_001199281|ref|NM_001201429|ens|ENST00000620406

NM_012295

Hs.517478

23523

CABIN1

calcineurin binding protein 1

ENST00000620406

Homo sapiens calcineurin binding protein 1 (CABIN1), transcript variant 2, mRNA [NM_012295]

chr22

24574422

24574481

A_33_P3373991

9.16

9.21

9.32

8.95

9.61

9.77

Detected

Hs.574600

ENST00000437095

17000424984468 GRN_ES Homo sapiens cDNA 5', mRNA sequence [CN283607]

chr2

233285490

233285431

A_33_P3266619

4.85

3.66

5.44

3.64

5.08

3.67

Not Detected

ens|ENST00000547602|ref|XR_245977|ref|XR_247813|ref|XR_253055

XR_245977

Hs.382689

728114

LOC728114

uncharacterized LOC728114

ENST00000547602

PREDICTED: Homo sapiens uncharacterized LOC728114 (LOC728114), misc_RNA [XR_245977]

chr12

48413644

48413585

A_33_P3361412

7.91

7.50

7.43

7.86

7.41

7.83

Detected

ref|NM_018420|ens|ENST00000369502|ens|ENST00000369503|ref|XR_426622

NM_018420

Hs.125482

55356

SLC22A15

solute carrier family 22, member 15

ENST00000369502

Homo sapiens solute carrier family 22, member 15 (SLC22A15), mRNA [NM_018420]

chr1

116569583

116569642

A_33_P3349927

7.36

7.11

7.03

7.29

7.44

7.25

Detected

ens|ENST00000467220|gb|CR627036|tc|NP1276298

CR627036

55112

WDR60

WD repeat domain 60

ENST00000467220

WD repeat domain 60 [Source:HGNC Symbol;Acc:HGNC:21862] [ENST00000467220]

chr7

158695283

158695342

A_22_P00023880

3.19

3.95

3.13

3.18

3.16

3.13

Not Detected

linc|lnc-ANKMY2-1:1|tc|THC2776638

lnc-ANKMY2-1

lnc-ANKMY2-1:1

Q3V199_MOUSE (Q3V199) 0 day neonate head cDNA, RIKEN full-length enriched library, clone:4833413M20 product:basic leucine zipper and W2 domains 2, full insert sequence. (Fragment), partial (13%) [THC2776638]

chr7

16735584

16735525

A_22_P00002594

6.69

7.44

6.68

7.02

6.84

6.29

Detected

linc|lnc-C19orf54-1:1

lnc-C19orf54-1

lnc-C19orf54-1:1

LNCipedia lincRNA (lnc-C19orf54-1), lincRNA [lnc-C19orf54-1:1]

chr19

41302261

41302202

A_22_P00019357

3.19

3.12

3.14

3.19

3.81

3.27

Not Detected

linc|lnc-UMPS-1:1|gb|BF727361

BF727361

Hs.581599

lnc-UMPS-1

lnc-UMPS-1:1

by20d10.y1 Human Lens cDNA (Un-normalized, unamplified): BY Homo sapiens cDNA clone by20d10 5', mRNA sequence [BF727361]

chr3

124506545

124506604

A_22_P00009095

6.47

5.60

6.15

8.69

6.00

5.45

Not Detected

Detected

linc|lnc-LHX2-2:1

lnc-LHX2-2

lnc-LHX2-2:1

LNCipedia lincRNA (lnc-LHX2-2), lincRNA [lnc-LHX2-2:1]

chr9

126514156

126514215

document location:

summary/2_Normlized_Data/NormalizedData.xlsx

3.2 Statistics of mRNA expression

Box-whisker Plot uses the five statistics in the data: the minimum, the first quartile (25%), the median (50%), the third quartile (75% ) and the maximum value to describe the data, it also can roughly see whether the data has the symmetry, the degree of distribution and other information.

document location:

summary/2_Normlized_Data/RNA_expression_boxplot.png

3.3 Differentially expressed mRNA

3.3.1 Profiling of differentially expressed mRNA

Differential expression of mRNA based on normalized signals was analyzed by selectively using Fisher exact test, Chi-squared 2x2 test, Chi-squared nxn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.

ProbeName	Treatment_1	Treatment_2	Treatment_3	Control_1	Control_2	Control_3	foldChange	log2FoldChange	regulation	pval	significant	PrimaryAccession	EntrezGeneID	GeneSymbol	GeneName	Description	chr	start	end	GO	KEGG
A_33_P3244165	19.49	19.49	19.49	19.49	19.49	19.49	1	0	down	0.00	yes	ref\|NR_003287\|ref\|NR_046235\|gb\|FB355642\|gb\|AK131444	100008589	RNA28S5	RNA, 28S ribosomal 5	Homo sapiens RNA, 28S ribosomal 5 (RNA28S5), ribosomal RNA [NR_003287]	chrUn_gl000220	117142	117201
A_23_P137097	10.46	10.46	10.68	8.12	8	8.06	1.31	0.39	up	0.00	yes	ref\|NM_006517\|ens\|ENST00000587091\|ref\|XM_005262294\|gb\|U05315	6567	SLC16A2	solute carrier family 16, member 2 (thyroid hormone transporter)	Homo sapiens solute carrier family 16, member 2 (thyroid hormone transporter) (SLC16A2), mRNA [NM_006517]	chrX	73753514	73753573	GO:0005215(transporter activity);GO:0005887(integral to plasma membrane);GO:0006810(transport);GO:0008028(monocarboxylic acid transmembrane transporter activity);GO:0015293(symporter activity);GO:0015349(thyroid hormone transmembrane transporter activity);GO:0015718(monocarboxylic acid transport);GO:0016020(membrane);GO:0016021(integral to membrane);GO:0034220(ion transmembrane transport);GO:0070327(thyroid hormone transport)	04919(Thyroid hormone signaling pathway)
A_32_P20454	12.19	12.12	12.19	11.11	11.20	11.10	1.09	0.13	up	0.00	yes	ref\|NM_001098398\|ref\|NM_004371\|gb\|CB240827	1314	COPA	coatomer protein complex, subunit alpha	Homo sapiens coatomer protein complex, subunit alpha (COPA), transcript variant 1, mRNA [NM_001098398]	chr1	160258482	160258423	GO:0005179(hormone activity);GO:0005198(structural molecule activity);GO:0005615(extracellular space);GO:0005737(cytoplasm);GO:0005829(cytosol);GO:0006886(intracellular protein transport);GO:0006890(retrograde vesicle-mediated transport, Golgi to ER);GO:0016020(membrane);GO:0030126(COPI vesicle coat);GO:0030157(pancreatic juice secretion);GO:0048205(COPI coating of Golgi vesicle);GO:0061024(membrane organization);GO:0070062(extracellular vesicular exosome)	04080(Neuroactive ligand-receptor interaction)
A_21_P0014329	12.18	12.21	12.17	11.16	11.10	11.27	1.09	0.12	up	0.00	yes	ens\|ENST00000563307\|gb\|BC053935\|gb\|AK090752\|gb\|AX746600	1459	CSNK2A2	casein kinase 2, alpha prime polypeptide	casein kinase 2, alpha prime polypeptide [Source:HGNC Symbol;Acc:HGNC:2459] [ENST00000563307]	chr16	58193554	58193495	GO:0000278(mitotic cell cycle);GO:0004674(protein serine/threonine kinase activity);GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-dependent);GO:0006355(regulation of transcription, DNA-dependent);GO:0006468(protein phosphorylation);GO:0006915(apoptotic process);GO:0007411(axon guidance);GO:0016055(Wnt receptor signaling pathway);GO:0031519(PcG protein complex);GO:0047485(protein N-terminus binding);GO:0071174(mitotic cell cycle spindle checkpoint)	03008(Ribosome biogenesis in eukaryotes\|04310:Wnt signaling pathway\|04064:NF-kappa B signaling pathway\|04520:Adherens junction\|04530:Tight junction\|05162:Measles\|05168:Herpes simplex infection\|05169:Epstein-Barr virus infection)
A_22_P00014850	10.50	10.74	10.68	9.12	8.97	8.95	1.18	0.24	up	0.00	yes	ens\|ENST00000607654\|ens\|ENST00000416861\|linc\|lnc-SLC4A3-1:1\|gb\|AK056734				Homo sapiens cDNA FLJ32172 fis, clone PLACE6000555. [AK056734]	chr2	220551715	220551774
A_23_P350574	11.73	11.71	11.78	11.26	11.24	11.31	1.04	0.06	up	0.00	yes	ref\|NM_001002901\|ref\|NM_001288831\|ref\|NM_001288832\|ref\|NM_001288829	127943	FCRLB	Fc receptor-like B	Homo sapiens Fc receptor-like B (FCRLB), transcript variant 1, mRNA [NM_001002901]	chr1	161697713	161697772	GO:0005737(cytoplasm);GO:0005783(endoplasmic reticulum);GO:0050777(negative regulation of immune response)
A_33_P3298539	11.50	11.53	11.44	12.65	12.47	12.46	0.92	-0.12	down	0.00	yes	ref\|NM_000039\|ens\|ENST00000236850\|ens\|ENST00000375323\|ens\|ENST00000375320	335	APOA1	apolipoprotein A-I	Homo sapiens apolipoprotein A-I (APOA1), mRNA [NM_000039]	chr11	116706700	116706641	GO:0001523(retinoid metabolic process);GO:0001540(beta-amyloid binding);GO:0001932(regulation of protein phosphorylation);GO:0001935(endothelial cell proliferation);GO:0002576(platelet degranulation);GO:0002740(negative regulation of cytokine secretion involved in immune response);GO:0005515(protein binding);GO:0005543(phospholipid binding);GO:0005548(phospholipid transporter activity);GO:0005576(extracellular region);GO:0005615(extracellular space);GO:0005634(nucleus);GO:0005769(early endosome);GO:0005788(endoplasmic reticulum lumen);GO:0005829(cytosol);GO:0005886(plasma membrane);GO:0006656(phosphatidylcholine biosynthetic process);GO:0006695(cholesterol biosynthetic process);GO:0006898(receptor-mediated endocytosis);GO:0007179(transforming growth factor beta receptor signaling pathway);GO:0007186(G-protein coupled receptor signaling pathway);GO:0007229(integrin-mediated signaling pathway);GO:0007584(response to nutrient);GO:0007596(blood coagulation);GO:0007603(phototransduction, visible light);GO:0008035(high-density lipoprotein particle binding);GO:0008203(cholesterol metabolic process);GO:0008211(glucocorticoid metabolic process);GO:0009986(cell surface);GO:0010804(negative regulation of tumor necrosis factor-mediated signaling pathway);GO:0010873(positive regulation of cholesterol esterification);GO:0010898(positive regulation of triglyceride catabolic process);GO:0010903(negative regulation of very-low-density lipoprotein particle remodeling);GO:0014012(peripheral nervous system axon regeneration);GO:0015485(cholesterol binding);GO:0017127(cholesterol transporter activity);GO:0018158(protein oxidation);GO:0018206(peptidyl-methionine modification);GO:0019899(enzyme binding);GO:0019915(lipid storage);GO:0030139(endocytic vesicle);GO:0030168(platelet activation);GO:0030300(regulation of intestinal cholesterol absorption);GO:0030301(cholesterol transport);GO:0030325(adrenal gland development);GO:0031100(organ regeneration);GO:0031102(neuron projection regeneration);GO:0031210(phosphatidylcholine binding);GO:0031410(cytoplasmic vesicle);GO:0031982(vesicle);GO:0032489(regulation of Cdc42 protein signal transduction);GO:0033344(cholesterol efflux);GO:0033700(phospholipid efflux);GO:0034115(negative regulation of heterotypic cell-cell adhesion);GO:0034190(apolipoprotein receptor binding);GO:0034191(apolipoprotein A-I receptor binding);GO:0034361(very-low-density lipoprotein particle);GO:0034364(high-density lipoprotein particle);GO:0034365(discoidal high-density lipoprotein particle);GO:0034366(spherical high-density lipoprotein particle);GO:0034375(high-density lipoprotein particle remodeling);GO:0034380(high-density lipoprotein particle assembly);GO:0034384(high-density lipoprotein particle clearance);GO:0034774(secretory granule lumen);GO:0035025(positive regulation of Rho protein signal transduction);GO:0042157(lipoprotein metabolic process);GO:0042158(lipoprotein biosynthetic process);GO:0042493(response to drug);GO:0042627(chylomicron);GO:0042632(cholesterol homeostasis);GO:0042802(identical protein binding);GO:0043534(blood vessel endothelial cell migration);GO:0043627(response to estrogen stimulus)	03320(PPAR signaling pathway\|04975:Fat digestion and absorption\|04977:Vitamin digestion and absorption\|05143:African trypanosomiasis)
A_23_P73801	10.79	10.76	10.84	10.26	10.29	10.34	1.05	0.07	up	0.00	yes	ref\|NM_001006640\|ref\|NM_004780\|ref\|NM_001006639\|ens\|ENST00000619397	9338	TCEAL1	transcription elongation factor A (SII)-like 1	Homo sapiens transcription elongation factor A (SII)-like 1 (TCEAL1), transcript variant 3, mRNA [NM_001006640]	chrX	102885333	102885392	GO:0000122(negative regulation of transcription from RNA polymerase II promoter);GO:0003700(sequence-specific DNA binding transcription factor activity);GO:0005634(nucleus);GO:0005654(nucleoplasm);GO:0006351(transcription, DNA-dependent)
A_23_P150238	12.96	12.87	12.98	13.59	13.67	13.57	0.95	-0.07	down	0.00	yes	ref\|NM_031450\|ref\|NM_001135635\|ens\|ENST00000449692\|ens\|ENST00000438576	83638	C11orf68	chromosome 11 open reading frame 68	Homo sapiens chromosome 11 open reading frame 68 (C11orf68), transcript variant 2, mRNA [NM_031450]	chr11	65684564	65684505
A_33_P3371425	12.85	12.85	12.81	13.24	13.19	13.27	0.97	-0.04	down	0.00	yes	ref\|NM_020451\|ref\|NM_206926\|ens\|ENST00000494537\|ens\|ENST00000354177	57190	SEPN1	selenoprotein N, 1	Homo sapiens selenoprotein N, 1 (SEPN1), transcript variant 1, mRNA [NM_020451]	chr1	26142117	26142176	GO:0003674(molecular_function);GO:0005509(calcium ion binding);GO:0005515(protein binding);GO:0005789(endoplasmic reticulum membrane);GO:0008150(biological_process)
A_22_P00013179	11.32	11.15	11.38	12.53	12.45	12.38	0.91	-0.14	down	0.00	yes	linc\|lnc-RNF144B-1:1\|gb\|AK098665\|tc\|THC2543869		lnc-RNF144B-1	lnc-RNF144B-1:1	Homo sapiens cDNA FLJ25799 fis, clone TST07088. [AK098665]	chr6	18536161	18536220
A_19_P00325810	7.79	7.90	7.62	9	8.94	8.95	0.87	-0.21	down	0.00	yes	ref\|NR_027005\|ens\|ENST00000484801\|gb\|AK090984\|tc\|THC2502979	80759	KHDC1	KH homology domain containing 1	Homo sapiens KH homology domain containing 1 (KHDC1), transcript variant 3, non-coding RNA [NR_027005]	chr6	73984736	73984677	GO:0003723(RNA binding);GO:0016021(integral to membrane)
A_21_P0009635	7.72	7.81	7.85	8.40	8.35	8.41	0.93	-0.11	down	0.00	yes	linc\|lnc-RTTN-2:1\|linc\|TCONS_00026726		lnc-RTTN-2	lnc-RTTN-2:1	LNCipedia lincRNA (lnc-RTTN-2), lincRNA [lnc-RTTN-2:1]	chr18	68004781	68004574
A_22_P00015934	9.73	9.82	9.80	9.15	9.03	9.16	1.07	0.10	up	0.00	yes	linc\|lnc-TCP11L2-2:1\|gb\|BG199486\|tc\|THC2776961		lnc-TCP11L2-2	lnc-TCP11L2-2:1	RST18770 Athersys RAGE Library Homo sapiens cDNA, mRNA sequence [BG199486]	chr12	106497094	106497153
A_24_P68631	13.57	13.50	13.52	14.26	14.31	14.45	0.94	-0.08	down	0.00	yes	ref\|NM_175065\|ens\|ENST00000331128\|gb\|BC172330\|gb\|BC132811	317772	HIST2H2AB	histone cluster 2, H2ab	Homo sapiens histone cluster 2, H2ab (HIST2H2AB), mRNA [NM_175065]	chr1	149859244	149859185	GO:0000786(nucleosome);GO:0003674(molecular_function);GO:0003677(DNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046982(protein heterodimerization activity);GO:0070062(extracellular vesicular exosome)	05322(Systemic lupus erythematosus\|05034:Alcoholism)
A_23_P88278	7.72	7.52	7.63	6.80	6.82	6.74	1.12	0.17	up	0.00	yes	ref\|NM_020366\|ens\|ENST00000400017\|ens\|ENST00000553927\|ens\|ENST00000555322	57096	RPGRIP1	retinitis pigmentosa GTPase regulator interacting protein 1	Homo sapiens retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1), mRNA [NM_020366]	chr14	21813303	21816336	GO:0005515(protein binding);GO:0005930(axoneme);GO:0007601(visual perception);GO:0032391(photoreceptor connecting cilium);GO:0042462(eye photoreceptor cell development);GO:0050896(response to stimulus);GO:0060041(retina development in camera-type eye)
A_33_P3808371	12.09	12.04	12.04	11.71	11.74	11.67	1.03	0.04	up	0.00	yes	gb\|AL833480\|gb\|AK125186\|tc\|THC2502358\|tc\|THC2566333	283911	LOC283911	uncharacterized LOC283911	Homo sapiens mRNA; cDNA DKFZp686C2429 (from clone DKFZp686C2429). [AL833480]	chr16	34388638	34388697
A_33_P3382423	8.37	8.30	8.32	7.76	7.72	7.61	1.08	0.11	up	0.00	yes	ref\|NM_182498\|ens\|ENST00000300811\|gb\|BC045799\|tc\|THC2472513	126299	ZNF428	zinc finger protein 428	Homo sapiens zinc finger protein 428 (ZNF428), mRNA [NM_182498]	chr19	44111451	44111392	GO:0046872(metal ion binding)
A_23_P68730	12.42	12.37	12.51	11.85	11.76	11.83	1.05	0.07	up	0.00	yes	ref\|NM_003681\|ens\|ENST00000291565\|ens\|ENST00000468090\|ref\|XM_005261198	8566	PDXK	pyridoxal (pyridoxine, vitamin B6) kinase	Homo sapiens pyridoxal (pyridoxine, vitamin B6) kinase (PDXK), mRNA [NM_003681]	chr21	45181808	45181867	GO:0000287(magnesium ion binding);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0005654(nucleoplasm);GO:0005737(cytoplasm);GO:0005829(cytosol);GO:0006766(vitamin metabolic process);GO:0006767(water-soluble vitamin metabolic process);GO:0008270(zinc ion binding);GO:0008283(cell proliferation);GO:0008478(pyridoxal kinase activity);GO:0009443(pyridoxal 5'-phosphate salvage);GO:0016310(phosphorylation);GO:0030170(pyridoxal phosphate binding);GO:0030955(potassium ion binding);GO:0031402(sodium ion binding);GO:0031403(lithium ion binding);GO:0042803(protein homodimerization activity);GO:0042816(vitamin B6 metabolic process);GO:0042823(pyridoxal phosphate biosynthetic process);GO:0044281(small molecule metabolic process);GO:0070062(extracellular vesicular exosome)	00750(Vitamin B6 metabolism)
A_33_P3214705	12.72	13.05	12.43	15.40	15.38	15.08	0.83	-0.26	down	0.00	yes	ref\|NM_001100418\|ref\|NM_001100419\|ens\|ENST00000597371\|ens\|ENST00000598375	55049	C19orf60	chromosome 19 open reading frame 60	Homo sapiens chromosome 19 open reading frame 60 (C19orf60), transcript variant 1, mRNA [NM_001100418]	chr19	18701688	18702918	GO:0005515(protein binding)
A_22_P00014845	10.94	11.13	11.06	10.31	10.22	10.19	1.08	0.11	up	0.00	yes	linc\|lnc-SLC4A10-2:1\|tc\|THC2638507		lnc-SLC4A10-2	lnc-SLC4A10-2:1	S79876 dipeptidyl peptidase IV {Homo sapiens} (exp=-1; wgp=0; cg=0), partial (94%) [THC2638507]	chr2	162929769	162929828
A_23_P31725	11.95	12.07	12.06	11.31	11.44	11.35	1.06	0.08	up	0.00	yes	ref\|NM_001715\|ens\|ENST00000526097\|ens\|ENST00000259089\|ref\|XM_005272390	640	BLK	BLK proto-oncogene, Src family tyrosine kinase	Homo sapiens BLK proto-oncogene, Src family tyrosine kinase (BLK), mRNA [NM_001715]	chr8	11421858	11421917	GO:0004713(protein tyrosine kinase activity);GO:0004715(non-membrane spanning protein tyrosine kinase activity);GO:0005102(receptor binding);GO:0005515(protein binding);GO:0005524(ATP binding);GO:0007169(transmembrane receptor protein tyrosine kinase signaling pathway);GO:0030217(T cell differentiation);GO:0031234(extrinsic to internal side of plasma membrane);GO:0032024(positive regulation of insulin secretion);GO:0035556(intracellular signal transduction);GO:0038083(peptidyl-tyrosine autophosphorylation);GO:0042127(regulation of cell proliferation);GO:0045087(innate immune response);GO:0050853(B cell receptor signaling pathway);GO:0071375(cellular response to peptide hormone stimulus)
A_21_P0014618	9.63	9.83	9.71	8.85	8.71	8.86	1.10	0.14	up	0.00	yes	ref\|XR_246615\|ref\|XR_249555\|ref\|XR_251536\|linc\|lnc-ATP5I-1:1	101928521	LOC101928521	uncharacterized LOC101928521	PREDICTED: Homo sapiens uncharacterized LOC101928521 (RP11-1191J2.2), ncRNA [XR_246615]	chr4	647379	647320
A_23_P64611	8.43	8.81	8.91	6.65	6.89	6.75	1.29	0.37	up	0.00	yes	ref\|NM_176798\|ref\|NM_001277204\|ref\|NM_176796\|ref\|NM_001277205	5031	P2RY6	pyrimidinergic receptor P2Y, G-protein coupled, 6	Homo sapiens pyrimidinergic receptor P2Y, G-protein coupled, 6 (P2RY6), transcript variant 2, mRNA [NM_176798]	chr11	73008625	73008684	GO:0004930(G-protein coupled receptor activity);GO:0005886(plasma membrane);GO:0005887(integral to plasma membrane);GO:0007200(phospholipase C-activating G-protein coupled receptor signaling pathway);GO:0014911(positive regulation of smooth muscle cell migration);GO:0016323(basolateral plasma membrane);GO:0016324(apical plasma membrane);GO:0030321(transepithelial chloride transport);GO:0035589(G-protein coupled purinergic nucleotide receptor signaling pathway);GO:0045028(G-protein coupled purinergic nucleotide receptor activity);GO:0045029(UDP-activated nucleotide receptor activity)	04080(Neuroactive ligand-receptor interaction)
A_22_P00006060	11.95	11.65	11.68	13.20	13.20	13.01	0.90	-0.16	down	0.00	yes	linc\|lnc-FAM131B-1:2\|gb\|AB074268\|gb\|CU690101\|tc\|THC2631669		lnc-FAM131B-1	lnc-FAM131B-1:2	Homo sapiens primary neuroblastoma cDNA, clone:Nbla10687, full insert sequence. [AB074268]	chr7	142983199	142983140
A_33_P3326872	8.58	8.69	8.67	7.86	7.94	8.03	1.09	0.12	up	0.00	yes						chr13	23411111	23411052
A_23_P351844	10.49	10.09	10.07	11.91	11.91	11.78	0.86	-0.22	down	0.00	yes	ref\|NM_001764\|ens\|ENST00000368168\|ens\|ENST00000451207\|gb\|M28826	910	CD1B	CD1b molecule	Homo sapiens CD1b molecule (CD1B), mRNA [NM_001764]	chr1	158297780	158297740	GO:0005515(protein binding);GO:0005765(lysosomal membrane);GO:0005886(plasma membrane);GO:0006955(immune response);GO:0009986(cell surface);GO:0010008(endosome membrane);GO:0016021(integral to membrane);GO:0030881(beta-2-microglobulin binding);GO:0030883(endogenous lipid antigen binding);GO:0030884(exogenous lipid antigen binding);GO:0048007(antigen processing and presentation, exogenous lipid antigen via MHC class Ib);GO:0071723(lipopeptide binding)	04640(Hematopoietic cell lineage)
A_23_P212458	13.78	13.76	13.69	13.40	13.38	13.34	1.03	0.04	up	0.00	yes	ref\|NM_013336\|ens\|ENST00000424880\|ens\|ENST00000243253\|ens\|ENST00000483956	29927	SEC61A1	Sec61 alpha 1 subunit (S. cerevisiae)	Homo sapiens Sec61 alpha 1 subunit (S. cerevisiae) (SEC61A1), mRNA [NM_013336]	chr3	127789960	127790019	GO:0002474(antigen processing and presentation of peptide antigen via MHC class I);GO:0002479(antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent);GO:0005515(protein binding);GO:0005791(rough endoplasmic reticulum);GO:0006614(SRP-dependent cotranslational protein targeting to membrane);GO:0006620(posttranslational protein targeting to membrane);GO:0007029(endoplasmic reticulum organization);GO:0016020(membrane);GO:0016049(cell growth);GO:0030176(integral to endoplasmic reticulum membrane);GO:0034341(response to interferon-gamma);GO:0042590(antigen processing and presentation of exogenous peptide antigen via MHC class I);GO:0043022(ribosome binding);GO:0045047(protein targeting to ER)	03060(Protein export\|04141:Protein processing in endoplasmic reticulum\|04145:Phagosome\|05110:Vibrio cholerae infection)
A_32_P213624	11.77	12.10	12.15	10.41	10.41	10.61	1.15	0.20	up	0.00	yes	ref\|NM_001130841\|ref\|NM_003729\|ens\|ENST00000370128\|ref\|XM_005271298	8634	RTCA	RNA 3'-terminal phosphate cyclase	Homo sapiens RNA 3'-terminal phosphate cyclase (RTCA), transcript variant 1, mRNA [NM_001130841]	chr1	100758204	100758263	GO:0003723(RNA binding);GO:0003963(RNA-3'-phosphate cyclase activity);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0005654(nucleoplasm);GO:0006396(RNA processing)
A_24_P392110	13.42	13.21	13.64	11.29	11.70	11.34	1.17	0.23	up	0.00	yes	ref\|NM_182707\|ref\|NM_001130167\|ref\|NM_001130168\|ref\|NM_021016	440533	PSG8	pregnancy specific beta-1-glycoprotein 8	Homo sapiens pregnancy specific beta-1-glycoprotein 8 (PSG8), transcript variant 1, mRNA [NM_182707]	chr19	43258549	43258490	GO:0005576(extracellular region)
A_22_P00012456	15.21	15.22	15.17	15.60	15.61	15.72	0.97	-0.04	down	0.00	yes	ref\|NR_027687\|ref\|NR_027686\|ens\|ENST00000431158\|ens\|ENST00000444463	284739	LINC00176	long intergenic non-protein coding RNA 176	Homo sapiens long intergenic non-protein coding RNA 176 (LINC00176), transcript variant 2, long non-coding RNA [NR_027687]	chr20	62669496	62669555
A_23_P103968	12.47	12.25	12.21	13.17	13.19	13.25	0.93	-0.10	down	0.00	yes	ref\|NM_012067\|ens\|ENST00000361640\|gb\|AF040639\|gb\|EU176235	22977	AKR7A3	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	Homo sapiens aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase) (AKR7A3), mRNA [NM_012067]	chr1	19611233	19610614	GO:0004033(aldo-keto reductase (NADP) activity);GO:0005829(cytosol);GO:0006081(cellular aldehyde metabolic process);GO:0006805(xenobiotic metabolic process);GO:0009055(electron carrier activity);GO:0044281(small molecule metabolic process);GO:0055114(oxidation-reduction process);GO:0070062(extracellular vesicular exosome)	00980(Metabolism of xenobiotics by cytochrome P450)
A_24_P357726	12.61	12.55	12.96	10.29	10.85	10.49	1.21	0.27	up	0.00	yes	ref\|NM_182707\|ref\|NM_001130167\|ref\|NM_001130168\|ref\|NM_002782	440533	PSG8	pregnancy specific beta-1-glycoprotein 8	Homo sapiens pregnancy specific beta-1-glycoprotein 8 (PSG8), transcript variant 1, mRNA [NM_182707]	chr19	43259206	43259147	GO:0005576(extracellular region)
A_33_P3330972	9.59	9.90	9.73	8.81	8.79	8.73	1.11	0.15	up	0.00	yes						chr4	624773	624714
A_23_P124427	9.41	9.44	9.56	10.63	11.06	10.93	0.87	-0.20	down	0.00	yes	ref\|NM_012224\|ref\|NM_001199397\|ref\|NM_001199398\|ref\|NM_001199400	4750	NEK1	NIMA-related kinase 1	Homo sapiens NIMA-related kinase 1 (NEK1), transcript variant 2, mRNA [NM_012224]	chr4	170315411	170315352	GO:0000165(MAPK cascade);GO:0000187(activation of MAPK activity);GO:0000242(pericentriolar material);GO:0004672(protein kinase activity);GO:0004674(protein serine/threonine kinase activity);GO:0004708(MAP kinase kinase activity);GO:0004713(protein tyrosine kinase activity);GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0005813(centrosome);GO:0006974(response to DNA damage stimulus);GO:0007067(mitosis);GO:0010212(response to ionizing radiation);GO:0018108(peptidyl-tyrosine phosphorylation);GO:0042384(cilium assembly);GO:0046872(metal ion binding);GO:0051301(cell division)
A_21_P0010240	7.37	7.43	7.59	8.22	8.17	8.14	0.91	-0.13	down	0.00	yes	ref\|XR_425268\|ref\|XR_430370\|ref\|XR_433641\|linc\|lnc-CHAF1B-1:1	102724630	LOC102724630	uncharacterized LOC102724630	PREDICTED: Homo sapiens uncharacterized LOC102724630 (LOC102724630), ncRNA [XR_425268]	chr21	37757138	37757197
A_32_P86763	14.47	14.54	14.34	13.66	13.78	13.77	1.05	0.07	up	0.00	yes	ref\|NM_004613\|ens\|ENST00000469269\|gb\|AK126508\|gb\|AK058031	7052	TGM2	transglutaminase 2	Homo sapiens transglutaminase 2 (TGM2), transcript variant 1, mRNA [NM_004613]	chr20	36757912	36757853	GO:0001974(blood vessel remodeling);GO:0003810(protein-glutamine gamma-glutamyltransferase activity);GO:0005515(protein binding);GO:0005525(GTP binding);GO:0005739(mitochondrion);GO:0005829(cytosol);GO:0005886(plasma membrane);GO:0005925(focal adhesion);GO:0018153(isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine);GO:0019904(protein domain specific binding);GO:0032471(reduction of endoplasmic reticulum calcium ion concentration);GO:0043065(positive regulation of apoptotic process);GO:0043123(positive regulation of I-kappaB kinase/NF-kappaB cascade);GO:0043277(apoptotic cell clearance);GO:0045785(positive regulation of cell adhesion);GO:0046872(metal ion binding);GO:0048661(positive regulation of smooth muscle cell proliferation);GO:0050729(positive regulation of inflammatory response);GO:0051260(protein homooligomerization);GO:0051482(elevation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway);GO:0051561(elevation of mitochondrial calcium ion concentration);GO:0060445(branching involved in salivary gland morphogenesis);GO:0060662(salivary gland cavitation);GO:0070062(extracellular vesicular exosome)	05016(Huntington's disease)
A_19_P00811706	8.10	8.51	8.18	6.82	6.48	6.62	1.24	0.32	up	0.00	yes	ref\|NM_005578\|ref\|NM_001167671\|ref\|NM_001167672\|ens\|ENST00000616304	4026	LPP	LIM domain containing preferred translocation partner in lipoma	Homo sapiens LIM domain containing preferred translocation partner in lipoma (LPP), transcript variant 1, mRNA [NM_005578]	chr3	188601619	188601678	GO:0005515(protein binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0005886(plasma membrane);GO:0005925(focal adhesion);GO:0007155(cell adhesion);GO:0008150(biological_process);GO:0008270(zinc ion binding)
A_32_P135336	6.82	6.82	6.75	7.46	7.55	7.34	0.91	-0.13	down	0.00	yes	ref\|NR_002556\|ref\|NR_002557\|ref\|XM_006726617\|tc\|THC2546736	388242	LOC388242	coiled-coil domain containing 101 pseudogene	Homo sapiens coiled-coil domain containing 101 pseudogene (LOC388242), non-coding RNA [NR_002556]	chr16	29476353	29476294
A_22_P00016477	8.03	8.29	8.16	7.41	7.33	7.31	1.11	0.15	up	0.00	yes	linc\|lnc-TMEM86A-1:1\|tc\|THC2607151		lnc-TMEM86A-1	lnc-TMEM86A-1:1	HSU27831 striatum-enriched phosphatase {Homo sapiens} (exp=-1; wgp=0; cg=0), partial (5%) [THC2607151]	chr11	18762025	18762084
A_19_P00812701	7.04	7.20	6.75	8.48	8.80	8.57	0.81	-0.30	down	0.00	yes						chr6	5041726	5041785
A_33_P3317825	12.87	12.68	12.86	13.42	13.43	13.48	0.95	-0.07	down	0.00	yes	ref\|NM_002524\|ens\|ENST00000369535\|gb\|AF493919\|gb\|BT019734	4893	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	Homo sapiens neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), mRNA [NM_002524]	chr1	115251224	115251165	GO:0000139(Golgi membrane);GO:0000165(MAPK cascade);GO:0000186(activation of MAPKK activity);GO:0005525(GTP binding);GO:0005886(plasma membrane);GO:0006184(GTP catabolic process);GO:0007173(epidermal growth factor receptor signaling pathway);GO:0007264(small GTPase mediated signal transduction);GO:0007265(Ras protein signal transduction);GO:0007411(axon guidance);GO:0007596(blood coagulation);GO:0008284(positive regulation of cell proliferation);GO:0008286(insulin receptor signaling pathway);GO:0008542(visual learning);GO:0008543(fibroblast growth factor receptor signaling pathway);GO:0016020(membrane);GO:0030036(actin cytoskeleton organization);GO:0032228(regulation of synaptic transmission, GABAergic);GO:0032403(protein complex binding);GO:0035022(positive regulation of Rac protein signal transduction);GO:0038095(Fc-epsilon receptor signaling pathway);GO:0043524(negative regulation of neuron apoptotic process);GO:0045087(innate immune response);GO:0045596(negative regulation of cell differentiation);GO:0048010(vascular endothelial growth factor receptor signaling pathway);GO:0048011(nerve growth factor receptor signaling pathway);GO:0048169(regulation of long-term neuronal synaptic plasticity);GO:0048642(negative regulation of skeletal muscle tissue development);GO:0050900(leukocyte migration);GO:0051146(striated muscle cell differentiation);GO:0060441(epithelial tube branching involved in lung morphogenesis);GO:0070062(extracellular vesicular exosome)	04014(Ras signaling pathway\|04015:Rap1 signaling pathway\|04010:MAPK signaling pathway\|04012:ErbB signaling pathway\|04370:VEGF signaling pathway\|04068:FoxO signaling pathway\|04071:Sphingolipid signaling pathway\|04151:PI3K-Akt signaling pathway\|04810:Regulation of actin cytoskeleton\|04530:Tight junction\|04540:Gap junction\|04550:Signaling pathways regulating pluripotency of stem cells\|04650:Natural killer cell mediated cytotoxicity\|04660:T cell receptor signaling pathway\|04662:B cell receptor signaling pathway\|04664:Fc epsilon RI signaling pathway\|04062:Chemokine signaling pathway\|04910:Insulin signaling pathway\|04912:GnRH signaling pathway\|04915:Estrogen signaling pathway\|04917:Prolactin signaling pathway\|04921:Oxytocin signaling pathway\|04919:Thyroid hormone signaling pathway\|04916:Melanogenesis\|04725:Cholinergic synapse\|04726:Serotonergic synapse\|04720:Long-term potentiation\|04730:Long-term depression\|04722:Neurotrophin signaling pathway\|04360:Axon guidance\|05200:Pathways in cancer\|05230:Central carbon metabolism in cancer\|05231:Choline metabolism in cancer\|05206:MicroRNAs in cancer\|05205:Proteoglycans in cancer\|05203:Viral carcinogenesis\|05214:Glioma\|05216:Thyroid cancer\|05221:Acute myeloid leukemia\|05220:Chronic myeloid leukemia\|05218:Melanoma\|05211:Renal cell carcinoma\|05219:Bladder cancer\|05215:Prostate cancer\|05213:Endometrial cancer\|05223:Non-small cell lung cancer\|05034:Alcoholism\|05166:HTLV-I infection\|05161:Hepatitis B\|05160:Hepatitis C)
A_33_P3407937	10.74	10.68	10.86	11.28	11.32	11.29	0.95	-0.07	down	0.00	yes	ref\|NM_018390\|ref\|NR_028057\|ens\|ENST00000381663\|ens\|ENST00000399012	55344	PLCXD1	phosphatidylinositol-specific phospholipase C, X domain containing 1	Homo sapiens phosphatidylinositol-specific phospholipase C, X domain containing 1 (PLCXD1), transcript variant 1, mRNA [NM_018390]	chrX	208260	208319	GO:0006629(lipid metabolic process);GO:0008081(phosphoric diester hydrolase activity)
A_24_P398064	12.45	12.56	12.60	12.09	12.05	12.02	1.04	0.06	up	0.00	yes	ens\|ENST00000378078\|gb\|D87447\|tc\|THC2514920	9827	RGP1	RGP1 retrograde golgi transport homolog (S. cerevisiae)	RGP1 retrograde golgi transport homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:21965] [ENST00000378078]	chr9	35757656	35757715	GO:0005515(protein binding);GO:0005829(cytosol);GO:0016020(membrane);GO:0017112(Rab guanyl-nucleotide exchange factor activity);GO:0017137(Rab GTPase binding);GO:0032851(positive regulation of Rab GTPase activity);GO:0034066(Ric1p-Rgp1p complex);GO:0042147(retrograde transport, endosome to Golgi);GO:0043234(protein complex)
A_32_P18250	13.60	13.60	13.67	13.13	13	13.16	1.04	0.06	up	0.00	yes	ref\|NR_003663\|ens\|ENST00000443452\|ens\|ENST00000331369\|gb\|BC040550	388965	FUNDC2P2	FUN14 domain containing 2 pseudogene 2	Homo sapiens FUN14 domain containing 2 pseudogene 2 (FUNDC2P2), non-coding RNA [NR_003663]	chr2	84518284	84518343
A_33_P3415430	13.10	13.08	13.26	13.78	13.81	13.71	0.95	-0.07	down	0.00	yes	ref\|NM_005346\|ens\|ENST00000545241\|ens\|ENST00000391548\|ens\|ENST00000375650	3304	HSPA1B	heat shock 70kDa protein 1B	Homo sapiens heat shock 70kDa protein 1B (HSPA1B), mRNA [NM_005346]	chr6	31797870	31797929	GO:0000151(ubiquitin ligase complex);GO:0001618(viral receptor activity);GO:0001664(G-protein coupled receptor binding);GO:0003725(double-stranded RNA binding);GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0005654(nucleoplasm);GO:0005737(cytoplasm);GO:0005739(mitochondrion);GO:0005783(endoplasmic reticulum);GO:0005814(centriole);GO:0005829(cytosol);GO:0005925(focal adhesion);GO:0006200(ATP catabolic process);GO:0006402(mRNA catabolic process);GO:0006986(response to unfolded protein);GO:0008180(signalosome);GO:0008285(negative regulation of cell proliferation);GO:0009615(response to virus);GO:0010467(gene expression);GO:0010941(regulation of cell death);GO:0016234(inclusion body);GO:0016235(aggresome);GO:0016607(nuclear speck);GO:0016887(ATPase activity);GO:0019899(enzyme binding);GO:0030308(negative regulation of cell growth);GO:0030529(ribonucleoprotein complex);GO:0031072(heat shock protein binding);GO:0031397(negative regulation of protein ubiquitination);GO:0031625(ubiquitin protein ligase binding);GO:0031982(vesicle);GO:0034599(cellular response to oxidative stress);GO:0034605(cellular response to heat);GO:0042026(protein refolding);GO:0042623(ATPase activity, coupled);GO:0043066(negative regulation of apoptotic process);GO:0044183(protein binding involved in protein folding);GO:0045648(positive regulation of erythrocyte differentiation);GO:0047485(protein N-terminus binding);GO:0048471(perinuclear region of cytoplasm);GO:0050821(protein stabilization);GO:0051082(unfolded protein binding);GO:0060548(negative regulation of cell death);GO:0070062(extracellular vesicular exosome);GO:0070370(cellular heat acclimation);GO:0072562(blood microparticle);GO:0090084(negative regulation of inclusion body assembly);GO:1900034(regulation of cellular response to heat);GO:2001240(negative regulation of extrinsic apoptotic signaling pathway in absence of ligand)	03040(Spliceosome\|04141:Protein processing in endoplasmic reticulum\|04010:MAPK signaling pathway\|04144:Endocytosis\|04612:Antigen processing and presentation\|04915:Estrogen signaling pathway\|05134:Legionellosis\|05162:Measles\|05164:Influenza A\|05169:Epstein-Barr virus infection\|05145:Toxoplasmosis)
A_22_P00015379	8.92	8.86	8.68	9.84	9.82	9.63	0.90	-0.15	down	0.00	yes	ref\|XR_424822\|ref\|XR_429964\|ref\|XR_430800\|ref\|XR_433386	101929494	LOC101929494	uncharacterized LOC101929494	PREDICTED: Homo sapiens uncharacterized LOC101929494 (LOC101929494), transcript variant X3, ncRNA [XR_424822]	chr17	36607637	36607578
A_23_P56228	10.68	11.02	10.88	11.92	11.79	11.85	0.92	-0.13	down	0.00	yes	ref\|NM_016573\|ref\|NM_001288999\|ref\|NM_001288998\|ens\|ENST00000203556	51291	GMIP	GEM interacting protein	Homo sapiens GEM interacting protein (GMIP), transcript variant 1, mRNA [NM_016573]	chr19	19740535	19740476	GO:0005100(Rho GTPase activator activity);GO:0005515(protein binding);GO:0005622(intracellular);GO:0005829(cytosol);GO:0007264(small GTPase mediated signal transduction);GO:0032321(positive regulation of Rho GTPase activity);GO:0034259(negative regulation of Rho GTPase activity);GO:0035556(intracellular signal transduction);GO:0046872(metal ion binding);GO:0051056(regulation of small GTPase mediated signal transduction)
A_21_P0008233	9.78	9.62	9.70	10.34	10.21	10.35	0.94	-0.09	down	0.00	yes	linc\|lnc-PABPC3-1:2\|linc\|lnc-PABPC3-1:1\|linc\|TCONS_00022147\|linc\|TCONS_00021734		lnc-PABPC3-1	lnc-PABPC3-1:2	LNCipedia lincRNA (lnc-PABPC3-1), lincRNA [lnc-PABPC3-1:2]	chr13	25692991	25693050
A_23_P360754	8.18	8.63	8.56	5.85	6.31	5.48	1.44	0.52	up	0.00	yes	ref\|NM_005099\|gb\|AB014588\|gb\|BC063293\|gb\|AY358886	9507	ADAMTS4	ADAM metallopeptidase with thrombospondin type 1 motif, 4	Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif, 4 (ADAMTS4), mRNA [NM_005099]	chr1	161159705	161159646	GO:0001501(skeletal system development);GO:0002020(protease binding);GO:0004222(metalloendopeptidase activity);GO:0005515(protein binding);GO:0005576(extracellular region);GO:0005578(proteinaceous extracellular matrix);GO:0005615(extracellular space);GO:0006508(proteolysis);GO:0008233(peptidase activity);GO:0008237(metallopeptidase activity);GO:0008270(zinc ion binding);GO:0022617(extracellular matrix disassembly);GO:0030198(extracellular matrix organization);GO:0031012(extracellular matrix);GO:0042742(defense response to bacterium)
A_33_P3336760	9.91	9.50	9.80	8.27	8.47	8.51	1.16	0.21	up	0.00	yes	ref\|NM_018849\|ref\|NM_000443\|ref\|NM_018850\|ens\|ENST00000265723	5244	ABCB4	ATP-binding cassette, sub-family B (MDR/TAP), member 4	Homo sapiens ATP-binding cassette, sub-family B (MDR/TAP), member 4 (ABCB4), transcript variant B, mRNA [NM_018849]	chr7	87031442	87031383	GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0005887(integral to plasma membrane);GO:0006629(lipid metabolic process);GO:0006810(transport);GO:0006855(drug transmembrane transport);GO:0008559(xenobiotic-transporting ATPase activity);GO:0016020(membrane);GO:0016021(integral to membrane);GO:0042493(response to drug);GO:0042626(ATPase activity, coupled to transmembrane movement of substances);GO:0042908(xenobiotic transport);GO:0044255(cellular lipid metabolic process);GO:0044281(small molecule metabolic process);GO:0046581(intercellular canaliculus);GO:0055085(transmembrane transport);GO:0070062(extracellular vesicular exosome)	02010(ABC transporters\|04976:Bile secretion)
A_23_P250136	7.48	6.83	7.52	4.33	3.94	3.31	1.89	0.91	up	0.00	yes	ref\|NM_175768\|ref\|NM_001166247\|ref\|NM_021956\|ens\|ENST00000369138	2898	GRIK2	glutamate receptor, ionotropic, kainate 2	Homo sapiens glutamate receptor, ionotropic, kainate 2 (GRIK2), transcript variant 2, mRNA [NM_175768]	chr6	102516621	102516680	GO:0001662(behavioral fear response);GO:0005234(extracellular-glutamate-gated ion channel activity);GO:0005886(plasma membrane);GO:0005887(integral to plasma membrane);GO:0006810(transport);GO:0006874(cellular calcium ion homeostasis);GO:0006886(intracellular protein transport);GO:0007215(glutamate receptor signaling pathway);GO:0007268(synaptic transmission);GO:0014069(postsynaptic density);GO:0015277(kainate selective glutamate receptor activity);GO:0019228(regulation of action potential in neuron);GO:0030054(cell junction);GO:0030165(PDZ domain binding);GO:0030425(dendrite);GO:0031624(ubiquitin conjugating enzyme binding);GO:0031625(ubiquitin protein ligase binding);GO:0032839(dendrite cytoplasm);GO:0032983(kainate selective glutamate receptor complex);GO:0034220(ion transmembrane transport);GO:0035235(ionotropic glutamate receptor signaling pathway);GO:0035249(synaptic transmission, glutamatergic);GO:0042734(presynaptic membrane);GO:0042803(protein homodimerization activity);GO:0043113(receptor clustering);GO:0043195(terminal button);GO:0043204(perikaryon);GO:0043524(negative regulation of neuron apoptotic process);GO:0043525(positive regulation of neuron apoptotic process);GO:0045211(postsynaptic membrane);GO:0046328(regulation of JNK cascade);GO:0048169(regulation of long-term neuronal synaptic plasticity);GO:0048172(regulation of short-term neuronal synaptic plasticity);GO:0050804(regulation of synaptic transmission);GO:0050806(positive regulation of synaptic transmission);GO:0051402(neuron apoptotic process);GO:0051967(negative regulation of synaptic transmission, glutamatergic);GO:0060079(regulation of excitatory postsynaptic membrane potential);GO:0060080(regulation of inhibitory postsynaptic membrane potential)	04080(Neuroactive ligand-receptor interaction\|04724:Glutamatergic synapse)
A_22_P00014149	7.44	7.10	7.01	9.12	8.66	9.02	0.80	-0.31	down	0.00	yes	ens\|ENST00000577329\|linc\|lnc-SCN4A-1:1					chr17	62050545	62050486
A_33_P3418025	9.33	9.24	9.62	7.79	8.08	8.12	1.18	0.23	up	0.00	yes	ref\|NM_001334\|ens\|ENST00000433477\|ens\|ENST00000573499\|gb\|BC049206	1519	CTSO	cathepsin O	Homo sapiens cathepsin O (CTSO), mRNA [NM_001334]	chr4	156845446	156845387	GO:0004197(cysteine-type endopeptidase activity);GO:0005764(lysosome);GO:0006508(proteolysis)	04142(Lysosome)
A_33_P3764744	9.65	9.04	9.21	11.37	11.18	11.01	0.83	-0.27	down	0.00	yes	tc\|THC2596880				HSU02032 ribosomal protein L23a {Homo sapiens} (exp=-1; wgp=0; cg=0), partial (70%) [THC2596880]	chr17	59148235	59148294	GO:0003723(RNA binding);GO:0003735(structural constituent of ribosome);GO:0005622(intracellular);GO:0006412(translation)
A_21_P0004977	10.53	10.49	10.58	11.07	10.96	11.14	0.95	-0.07	down	0.00	yes	linc\|lnc-FAM120B-6:2\|linc\|TCONS_00012028		lnc-FAM120B-6	lnc-FAM120B-6:2	LNCipedia lincRNA (lnc-FAM120B-6), lincRNA [lnc-FAM120B-6:2]	chr6	170455160	170455219
A_23_P65129	10.99	10.65	10.78	11.84	11.70	11.75	0.92	-0.12	down	0.00	yes	ref\|NM_032840\|ens\|ENST00000301463\|gb\|BC136312\|gb\|AK027706	84926	SPRYD3	SPRY domain containing 3	Homo sapiens SPRY domain containing 3 (SPRYD3), mRNA [NM_032840]	chr12	53458705	53458646
A_24_P309645	12.52	12.46	12.51	11.44	11.78	11.59	1.08	0.11	up	0.00	yes	ref\|NM_017901\|ref\|NM_001143819\|ref\|NM_001301214\|ens\|ENST00000551127	53373	TPCN1	two pore segment channel 1	Homo sapiens two pore segment channel 1 (TPCN1), transcript variant 2, mRNA [NM_017901]	chr12	113730870	113731124	GO:0005245(voltage-gated calcium channel activity);GO:0005515(protein binding);GO:0005765(lysosomal membrane);GO:0005886(plasma membrane);GO:0006816(calcium ion transport);GO:0010008(endosome membrane);GO:0016021(integral to membrane);GO:0034220(ion transmembrane transport);GO:0034765(regulation of ion transmembrane transport);GO:0042802(identical protein binding);GO:0055085(transmembrane transport);GO:0070588(calcium ion transmembrane transport);GO:0072345(NAADP-sensitive calcium-release channel activity);GO:0086010(membrane depolarization involved in regulation of action potential)
A_22_P00005067	5.80	5.50	5.68	4.67	4.46	4.33	1.26	0.34	up	0.00	yes	ens\|ENST00000545293\|ens\|ENST00000543611\|linc\|lnc-DENR-2:2\|linc\|lnc-DENR-2:1					chr12	123200160	123200219
A_23_P169112	11.77	11.51	11.52	12.47	12.58	12.72	0.92	-0.12	down	0.00	yes	ref\|NM_013291\|ens\|ENST00000526271\|ens\|ENST00000620219\|ens\|ENST00000616140	29894	CPSF1	cleavage and polyadenylation specific factor 1, 160kDa	Homo sapiens cleavage and polyadenylation specific factor 1, 160kDa (CPSF1), mRNA [NM_013291]	chr8	145619722	145619663	GO:0000398(nuclear mRNA splicing, via spliceosome);GO:0003730(mRNA 3'-UTR binding);GO:0005515(protein binding);GO:0005654(nucleoplasm);GO:0005847(mRNA cleavage and polyadenylation specificity factor complex);GO:0006366(transcription from RNA polymerase II promoter);GO:0006369(termination of RNA polymerase II transcription);GO:0006378(mRNA polyadenylation);GO:0006379(mRNA cleavage);GO:0006406(mRNA export from nucleus);GO:0008380(RNA splicing);GO:0010467(gene expression);GO:0031124(mRNA 3'-end processing)	03015(mRNA surveillance pathway)
A_23_P46039	7.66	6.72	8.10	3.88	3.32	3.22	2.16	1.11	up	0.00	yes	ref\|NM_032738\|ref\|NM_001184866\|ref\|NM_001184867\|ref\|NM_001184870	84824	FCRLA	Fc receptor-like A	Homo sapiens Fc receptor-like A (FCRLA), transcript variant 2, mRNA [NM_032738]	chr1	161683792	161683851	GO:0005576(extracellular region);GO:0005737(cytoplasm);GO:0030154(cell differentiation)
A_22_P00007531	12.15	12.09	12.15	11.78	11.63	11.66	1.04	0.05	up	0.00	yes	ref\|NR_029373\|ref\|NR_029374\|linc\|lnc-HADH-1:3\|linc\|lnc-HADH-1:1	641518	LEF1-AS1	LEF1 antisense RNA 1	Homo sapiens LEF1 antisense RNA 1 (LEF1-AS1), transcript variant 1, long non-coding RNA [NR_029373]	chr4	109097484	109097543
A_33_P3341442	10.33	10.10	9.98	11.32	11.23	11.09	0.90	-0.15	down	0.00	yes	ref\|NM_000395\|ens\|ENST00000262825\|ens\|ENST00000403662\|ref\|XM_005261340	1439	CSF2RB	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	Homo sapiens colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) (CSF2RB), mRNA [NM_000395]	chr22	37334388	37334447	GO:0004872(receptor activity);GO:0004912(interleukin-3 receptor activity);GO:0004914(interleukin-5 receptor activity);GO:0005515(protein binding);GO:0005886(plasma membrane);GO:0005887(integral to plasma membrane);GO:0007165(signal transduction);GO:0007585(respiratory gaseous exchange);GO:0030526(granulocyte macrophage colony-stimulating factor receptor complex);GO:0032496(response to lipopolysaccharide);GO:0036016(cellular response to interleukin-3);GO:0038043(interleukin-5-mediated signaling pathway);GO:0038156(interleukin-3-mediated signaling pathway)	04630(Jak-STAT signaling pathway\|04060:Cytokine-cytokine receptor interaction\|04210:Apoptosis)
A_24_P265088	10.04	10.08	10.27	9.44	9.26	9.27	1.09	0.12	up	0.00	yes	ens\|ENST00000393758\|ens\|ENST00000544474\|ens\|ENST00000164640\|gb\|AK127016	57595	PDZD4	PDZ domain containing 4	PDZ domain containing 4 [Source:HGNC Symbol;Acc:HGNC:21167] [ENST00000393758]	chrX	153068362	153068303	GO:0005938(cell cortex)
A_33_P3374559	10.93	11.14	10.89	12.21	12.18	12.59	0.89	-0.17	down	0.00	yes	ref\|NR_024448\|ens\|ENST00000444220\|ens\|ENST00000437294\|ens\|ENST00000435868	91316	GUSBP11	glucuronidase, beta pseudogene 11	Homo sapiens glucuronidase, beta pseudogene 11 (GUSBP11), non-coding RNA [NR_024448]	chr22	24057258	24057199
A_33_P3316728	7.26	7.31	7.31	7.64	7.65	7.77	0.95	-0.08	down	0.00	yes	ens\|ENST00000567850\|ens\|ENST00000564895				DNM1 pseudogene 34 [Source:HGNC Symbol;Acc:HGNC:35181] [ENST00000567850]	chr15	75594935	75594876
A_24_P333663	12.54	12.51	12.85	11.46	11.12	11.39	1.12	0.16	up	0.00	yes	ref\|NM_002748\|ens\|ENST00000518703\|ens\|ENST00000403865\|ref\|XM_005254536	5597	MAPK6	mitogen-activated protein kinase 6	Homo sapiens mitogen-activated protein kinase 6 (MAPK6), mRNA [NM_002748]	chr15	52356907	52356966	GO:0000165(MAPK cascade);GO:0004674(protein serine/threonine kinase activity);GO:0004707(MAP kinase activity);GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006468(protein phosphorylation);GO:0007049(cell cycle);GO:0007165(signal transduction);GO:0019901(protein kinase binding);GO:0046982(protein heterodimerization activity)
A_22_P00018902	11.21	11.46	11.35	10.36	10.57	10.54	1.08	0.11	up	0.00	yes	linc\|lnc-C11orf39-3:1\|gb\|DA375949		lnc-C11orf39-3	lnc-C11orf39-3:1	DA375949 BRTHA2 Homo sapiens cDNA clone BRTHA2007423 5', mRNA sequence [DA375949]	chr11	131747657	131747598
A_21_P0008490	10.97	11.82	10.76	14.57	14.55	14.03	0.78	-0.36	down	0.00	yes	linc\|lnc-RTL1-6:1\|linc\|TCONS_00022880		lnc-RTL1-6	lnc-RTL1-6:1	LNCipedia lincRNA (lnc-RTL1-6), lincRNA [lnc-RTL1-6:1]	chr14	101820284	101820225
A_33_P3226377	11.72	11.89	11.76	11.35	11.28	11.30	1.04	0.06	up	0.00	yes	ref\|NM_005042\|ref\|NM_001110213\|ens\|ENST00000381847\|ens\|ENST00000575657	5555	PRH2	proline-rich protein HaeIII subfamily 2	Homo sapiens proline-rich protein HaeIII subfamily 2 (PRH2), transcript variant 1, mRNA [NM_005042]	chr12	11083624	11083683	GO:0005515(protein binding);GO:0005615(extracellular space)	04970(Salivary secretion)
A_33_P3257568	7.07	6.97	6.72	7.87	7.95	7.82	0.88	-0.19	down	0.00	yes	ens\|ENST00000373851\|gb\|AK097636\|tc\|THC2721284	11064	CNTRL	centriolin	centriolin [Source:HGNC Symbol;Acc:HGNC:1858] [ENST00000373851]	chr9	123912863	123912922	GO:0000086(G2/M transition of mitotic cell cycle);GO:0000278(mitotic cell cycle);GO:0005515(protein binding);GO:0005737(cytoplasm);GO:0005813(centrosome);GO:0005829(cytosol);GO:0006996(organelle organization);GO:0016020(membrane);GO:0051301(cell division)
A_22_P00011020	10.81	10.80	10.71	11.51	11.54	11.31	0.94	-0.09	down	0.00	yes	linc\|lnc-NT5C-2:1		lnc-NT5C-2	lnc-NT5C-2:1	LNCipedia lincRNA (lnc-NT5C-2), lincRNA [lnc-NT5C-2:1]	chr17	73141416	73141357
A_33_P3346403	17.59	17.59	17.48	17.89	17.92	17.97	0.98	-0.03	down	0.00	yes	ref\|NM_001099285\|ref\|NM_002823\|ens\|ENST00000397729\|ens\|ENST00000393073	5757	PTMA	prothymosin, alpha	Homo sapiens prothymosin, alpha (PTMA), transcript variant 1, mRNA [NM_001099285]	chr2	232577214	232577560	GO:0005515(protein binding);GO:0005634(nucleus);GO:0005654(nucleoplasm);GO:0005737(cytoplasm);GO:0006351(transcription, DNA-dependent);GO:0070062(extracellular vesicular exosome)	05169(Epstein-Barr virus infection)
A_33_P3266646	8.38	8.50	8.52	9.07	9.01	9.21	0.93	-0.10	down	0.00	yes	ref\|NM_138813\|ref\|NM_001178002\|ref\|NR_047593\|ens\|ENST00000533107	148229	ATP8B3	ATPase, aminophospholipid transporter, class I, type 8B, member 3	Homo sapiens ATPase, aminophospholipid transporter, class I, type 8B, member 3 (ATP8B3), transcript variant 1, mRNA [NM_138813]	chr19	1800003	1797004	GO:0000287(magnesium ion binding);GO:0002080(acrosomal membrane);GO:0004012(phospholipid-translocating ATPase activity);GO:0005524(ATP binding);GO:0005783(endoplasmic reticulum);GO:0005794(Golgi apparatus);GO:0005886(plasma membrane);GO:0007030(Golgi organization);GO:0007339(binding of sperm to zona pellucida);GO:0008152(metabolic process);GO:0016021(integral to membrane);GO:0045332(phospholipid translocation)
A_23_P104689	11.77	11.67	11.65	11.21	11.32	11.29	1.04	0.05	up	0.00	yes	ref\|NM_021975\|ref\|NM_001145138\|ref\|NM_001243984\|ref\|NM_001243985	5970	RELA	v-rel avian reticuloendotheliosis viral oncogene homolog A	Homo sapiens v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), transcript variant 1, mRNA [NM_021975]	chr11	65421710	65421651	GO:0000122(negative regulation of transcription from RNA polymerase II promoter);GO:0000978(RNA polymerase II core promoter proximal region sequence-specific DNA binding);GO:0000980(RNA polymerase II distal enhancer sequence-specific DNA binding);GO:0001077(RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription);GO:0001078(RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription);GO:0001205(RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription);GO:0001889(liver development);GO:0001942(hair follicle development);GO:0002224(toll-like receptor signaling pathway);GO:0002755(MyD88-dependent toll-like receptor signaling pathway);GO:0002756(MyD88-independent toll-like receptor signaling pathway);GO:0003677(DNA binding);GO:0003682(chromatin binding);GO:0003700(sequence-specific DNA binding transcription factor activity);GO:0003705(RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity);GO:0005515(protein binding);GO:0005634(nucleus);GO:0005654(nucleoplasm);GO:0005667(transcription factor complex);GO:0005737(cytoplasm);GO:0005829(cytosol);GO:0006117(acetaldehyde metabolic process);GO:0006366(transcription from RNA polymerase II promoter);GO:0006954(inflammatory response);GO:0006968(cellular defense response);GO:0007568(aging);GO:0008134(transcription factor binding);GO:0008284(positive regulation of cell proliferation);GO:0009612(response to mechanical stimulus);GO:0009887(organ morphogenesis);GO:0010033(response to organic substance);GO:0010224(response to UV-B);GO:0014040(positive regulation of Schwann cell differentiation);GO:0016032(viral reproduction);GO:0019221(cytokine-mediated signaling pathway);GO:0019901(protein kinase binding);GO:0031293(membrane protein intracellular domain proteolysis);GO:0031625(ubiquitin protein ligase binding);GO:0032332(positive regulation of chondrocyte differentiation);GO:0032403(protein complex binding);GO:0032481(positive regulation of type I interferon production);GO:0032495(response to muramyl dipeptide);GO:0032570(response to progesterone stimulus);GO:0032868(response to insulin stimulus);GO:0033256(I-kappaB/NF-kappaB complex);GO:0033590(response to cobalamin);GO:0033613(activating transcription factor binding);GO:0034134(toll-like receptor 2 signaling pathway);GO:0034138(toll-like receptor 3 signaling pathway);GO:0034142(toll-like receptor 4 signaling pathway);GO:0034146(toll-like receptor 5 signaling pathway);GO:0034162(toll-like receptor 9 signaling pathway);GO:0034166(toll-like receptor 10 signaling pathway);GO:0035666(TRIF-dependent toll-like receptor signaling pathway);GO:0038061(NIK/NF-kappaB cascade);GO:0038095(Fc-epsilon receptor signaling pathway);GO:0038123(toll-like receptor TLR1:TLR2 signaling pathway);GO:0038124(toll-like receptor TLR6:TLR2 signaling pathway)	04014(Ras signaling pathway\|04010:MAPK signaling pathway\|04064:NF-kappa B signaling pathway\|04668:TNF signaling pathway\|04066:HIF-1 signaling pathway\|04071:Sphingolipid signaling pathway\|04024:cAMP signaling pathway\|04151:PI3K-Akt signaling pathway\|04210:Apoptosis\|04620:Toll-like receptor signaling pathway\|04621:NOD-like receptor signaling pathway\|04622:RIG-I-like receptor signaling pathway\|04623:Cytosolic DNA-sensing pathway\|04660:T cell receptor signaling pathway\|04662:B cell receptor signaling pathway\|04062:Chemokine signaling pathway\|04920:Adipocytokine signaling pathway\|04917:Prolactin signaling pathway\|04722:Neurotrophin signaling pathway\|04380:Osteoclast differentiation\|05200:Pathways in cancer\|05202:Transcriptional misregulation in cancers\|05203:Viral carcinogenesis\|05212:Pancreatic cancer\|05221:Acute myeloid leukemia\|05220:Chronic myeloid leukemia\|05215:Prostate cancer\|05222:Small cell lung cancer\|05321:Inflammatiory bowel disease (IBD)\|05030:Cocaine addiction\|04932:Non-alcoholic fatty liver disease (NAFLD)\|05120:Epithelial cell signaling in Helicobacter pylori infection\|05132:Salmonella infection\|05131:Shigellosis\|05133:Pertussis\|05134:Legionellosis\|05152:Tuberculosis\|05166:HTLV-I infection\|05162:Measles\|05164:Influenza A\|05161:Hepatitis B\|05160:Hepatitis C\|05168:Herpes simplex infection\|05169:Epstein-Barr virus infection\|05146:Amoebiasis\|05145:Toxoplasmosis\|05140:Leishmaniasis\|05142:Chagas disease (American trypanosomiasis))
A_32_P160896	14.12	14.55	14.36	11.32	12.05	10.98	1.25	0.33	up	0.00	yes	ref\|NM_177478\|ens\|ENST00000321339\|gb\|HQ258558\|gb\|BC034419	94033	FTMT	ferritin mitochondrial	Homo sapiens ferritin mitochondrial (FTMT), mRNA [NM_177478]	chr5	121188259	121188318	GO:0004322(ferroxidase activity);GO:0005634(nucleus);GO:0005739(mitochondrion);GO:0006826(iron ion transport);GO:0006879(cellular iron ion homeostasis);GO:0008199(ferric iron binding);GO:0008284(positive regulation of cell proliferation);GO:0051347(positive regulation of transferase activity);GO:0051349(positive regulation of lyase activity);GO:0051353(positive regulation of oxidoreductase activity);GO:0055114(oxidation-reduction process)
A_21_P0001177	11.71	11.56	12.27	9.79	9.59	9.23	1.24	0.31	up	0.00	yes	linc\|lnc-FAM72C-2:1\|ref\|XM_006711090\|ref\|XM_006726339\|linc\|TCONS_00000639		lnc-FAM72C-2	lnc-FAM72C-2:1	PREDICTED: Homo sapiens myomegalin-like (LOC100996723), mRNA [XM_006711090]	chr1	144506631	144506690
A_33_P3257714	10.65	10.72	10.92	9.83	10.01	9.97	1.08	0.12	up	0.00	yes	ref\|NM_001025\|ens\|ENST00000296674\|gb\|M32219\|gb\|BX647563	6228	RPS23	ribosomal protein S23	Homo sapiens ribosomal protein S23 (RPS23), mRNA [NM_001025]	chr5	81569349	81569290	GO:0000184(nuclear-transcribed mRNA catabolic process, nonsense-mediated decay);GO:0003735(structural constituent of ribosome);GO:0005515(protein binding);GO:0005730(nucleolus);GO:0005737(cytoplasm);GO:0005829(cytosol);GO:0005840(ribosome);GO:0006412(translation);GO:0006413(translational initiation);GO:0006414(translational elongation);GO:0006415(translational termination);GO:0006614(SRP-dependent cotranslational protein targeting to membrane);GO:0010467(gene expression);GO:0016020(membrane);GO:0016032(viral reproduction);GO:0019058(viral infectious cycle);GO:0019083(viral transcription);GO:0022627(cytosolic small ribosomal subunit);GO:0044267(cellular protein metabolic process)	03010(Ribosome)
A_33_P3394395	10.82	11.09	11.26	9.80	9.62	9.90	1.13	0.18	up	0.00	yes	ref\|NM_001270384\|ref\|NM_198549\|ens\|ENST00000370791\|ens\|ENST00000443751	374986	FAM73A	family with sequence similarity 73, member A	Homo sapiens family with sequence similarity 73, member A (FAM73A), transcript variant 2, mRNA [NM_001270384]	chr1	78343754	78343813	GO:0016021(integral to membrane)
A_22_P00012557	7.73	7.98	7.92	7.14	7.17	7.25	1.10	0.13	up	0.00	yes	ref\|NR_033374\|linc\|lnc-PTGES2-1:4\|linc\|lnc-PTGES2-1:1\|linc\|lnc-PTGES2-1:5	100289019	SLC25A25-AS1	SLC25A25 antisense RNA 1	Homo sapiens SLC25A25 antisense RNA 1 (SLC25A25-AS1), long non-coding RNA [NR_033374]	chr9	130876872	130876813
A_19_P00322898	12.23	12.23	12.21	11.98	11.99	11.89	1.02	0.03	up	0.00	yes	ref\|NR_026551\|ens\|ENST00000448692\|ens\|ENST00000380333\|tc\|THC2501410	340591	CA5BP1	carbonic anhydrase VB pseudogene 1	Homo sapiens carbonic anhydrase VB pseudogene 1 (CA5BP1), non-coding RNA [NR_026551]	chrX	15693842	15693901	GO:0004089(carbonate dehydratase activity);GO:0005739(mitochondrion);GO:0008152(metabolic process);GO:0008270(zinc ion binding)
A_23_P57868	11.50	11.31	11.25	12.28	12.57	12.67	0.91	-0.14	down	0.00	yes	ref\|NM_000666\|ref\|NM_001198895\|ref\|NM_001198898\|ref\|NM_001198897	95	ACY1	aminoacylase 1	Homo sapiens aminoacylase 1 (ACY1), transcript variant 1, mRNA [NM_000666]	chr3	52022979	52023038	GO:0004046(aminoacylase activity);GO:0005829(cytosol);GO:0006508(proteolysis);GO:0006520(cellular amino acid metabolic process);GO:0006805(xenobiotic metabolic process);GO:0008237(metallopeptidase activity);GO:0044281(small molecule metabolic process);GO:0046872(metal ion binding);GO:0070062(extracellular vesicular exosome)	01210(2-Oxocarboxylic acid metabolism\|01230:Biosynthesis of amino acids\|00330:Arginine and proline metabolism)
A_23_P149494	12.37	11.98	12.46	11.02	10.89	11.05	1.12	0.16	up	0.00	yes	ref\|NM_015600\|ref\|NM_001042472\|ens\|ENST00000481556\|ens\|ENST00000376542	26090	ABHD12	abhydrolase domain containing 12	Homo sapiens abhydrolase domain containing 12 (ABHD12), transcript variant 2, mRNA [NM_015600]	chr20	25288665	25288606	GO:0006660(phosphatidylserine catabolic process);GO:0007628(adult walking behavior);GO:0010996(response to auditory stimulus);GO:0032281(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex);GO:0047372(acylglycerol lipase activity)
A_24_P212129	10.94	10.94	11.02	11.45	11.64	11.68	0.95	-0.08	down	0.00	yes	ref\|NM_006974\|ref\|NM_001278170\|ref\|NM_001278173\|ref\|NM_001278178	7581	ZNF33A	zinc finger protein 33A	Homo sapiens zinc finger protein 33A (ZNF33A), transcript variant 2, mRNA [NM_006974]	chr10	38306221	38306280	GO:0003677(DNA binding);GO:0003700(sequence-specific DNA binding transcription factor activity);GO:0005634(nucleus);GO:0006351(transcription, DNA-dependent);GO:0006355(regulation of transcription, DNA-dependent);GO:0046872(metal ion binding)
A_32_P221799	11.41	11.46	11.05	13	12.58	12.98	0.88	-0.18	down	0.00	yes	ref\|NM_003514\|gb\|BC071668\|gb\|BC032686\|gb\|BC032756	8336	HIST1H2AM	histone cluster 1, H2am	Homo sapiens histone cluster 1, H2am (HIST1H2AM), mRNA [NM_003514]	chr6	27860566	27860507	GO:0000786(nucleosome);GO:0003677(DNA binding);GO:0005515(protein binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0019899(enzyme binding);GO:0046982(protein heterodimerization activity);GO:0070062(extracellular vesicular exosome)	05322(Systemic lupus erythematosus\|05034:Alcoholism)
A_33_P3353030	10.98	10.88	11.11	10.30	10.04	10.10	1.08	0.12	up	0.00	yes	ref\|NM_003353\|ens\|ENST00000296099\|tc\|THC2476757	7349	UCN	urocortin	Homo sapiens urocortin (UCN), mRNA [NM_003353]	chr2	27530324	27530265	GO:0005184(neuropeptide hormone activity);GO:0005515(protein binding);GO:0005576(extracellular region);GO:0006954(inflammatory response);GO:0006979(response to oxidative stress);GO:0007186(G-protein coupled receptor signaling pathway);GO:0007218(neuropeptide signaling pathway);GO:0007565(female pregnancy);GO:0007605(sensory perception of sound);GO:0008306(associative learning);GO:0009060(aerobic respiration);GO:0010629(negative regulation of gene expression);GO:0030157(pancreatic juice secretion);GO:0030307(positive regulation of cell growth);GO:0030425(dendrite);GO:0030819(positive regulation of cAMP biosynthetic process);GO:0031064(negative regulation of histone deacetylation);GO:0031175(neuron projection development);GO:0032099(negative regulation of appetite);GO:0032355(response to estradiol stimulus);GO:0032755(positive regulation of interleukin-6 production);GO:0032967(positive regulation of collagen biosynthetic process);GO:0033138(positive regulation of peptidyl-serine phosphorylation);GO:0034199(activation of protein kinase A activity);GO:0035176(social behavior);GO:0035483(gastric emptying);GO:0042756(drinking behavior);GO:0043066(negative regulation of apoptotic process);GO:0043117(positive regulation of vascular permeability);GO:0043196(varicosity);GO:0043204(perikaryon);GO:0043679(axon terminus);GO:0045727(positive regulation of translation);GO:0045740(positive regulation of DNA replication);GO:0045776(negative regulation of blood pressure);GO:0045792(negative regulation of cell size);GO:0045909(positive regulation of vasodilation);GO:0046811(histone deacetylase inhibitor activity);GO:0046888(negative regulation of hormone secretion);GO:0048265(response to pain);GO:0051384(response to glucocorticoid stimulus);GO:0051430(corticotropin-releasing hormone receptor 1 binding);GO:0051431(corticotropin-releasing hormone receptor 2 binding);GO:0051461(positive regulation of corticotropin secretion);GO:0051966(regulation of synaptic transmission, glutamatergic);GO:0060452(positive regulation of cardiac muscle contraction);GO:0060455(negative regulation of gastric acid secretion);GO:0060547(negative regulation of necrotic cell death);GO:0090280(positive regulation of calcium ion import);GO:2000252(negative regulation of feeding behavior);GO:2000987(positive regulation of behavioral fear response)
A_22_P00002714	10.71	10.27	10.35	12.15	11.87	11.74	0.88	-0.19	down	0.00	yes	ens\|ENST00000437035\|ens\|ENST00000421257\|linc\|lnc-C20orf197-3:9\|linc\|lnc-C20orf197-3:10				MIR646 host gene (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:27659] [ENST00000437035]	chr20	58888386	58888445
A_33_P3392537	9.33	9.30	9.65	6.84	7.08	7.68	1.31	0.39	up	0.00	yes	ref\|NM_004614\|ref\|NM_001172645\|ref\|NM_001172644\|ref\|NM_001172643	7084	TK2	thymidine kinase 2, mitochondrial	Homo sapiens thymidine kinase 2, mitochondrial (TK2), transcript variant 1, mRNA [NM_004614]	chr16	66543411	66543352	GO:0004137(deoxycytidine kinase activity);GO:0004797(thymidine kinase activity);GO:0005524(ATP binding);GO:0005743(mitochondrial inner membrane);GO:0005759(mitochondrial matrix);GO:0006139(nucleobase-containing compound metabolic process);GO:0006206(pyrimidine base metabolic process);GO:0006264(mitochondrial DNA replication);GO:0009157(deoxyribonucleoside monophosphate biosynthetic process);GO:0009165(nucleotide biosynthetic process);GO:0009262(deoxyribonucleotide metabolic process);GO:0016310(phosphorylation);GO:0043097(pyrimidine nucleoside salvage);GO:0044281(small molecule metabolic process);GO:0046092(deoxycytidine metabolic process);GO:0046104(thymidine metabolic process);GO:0055086(nucleobase-containing small molecule metabolic process);GO:0071897(DNA biosynthetic process)	00240(Pyrimidine metabolism\|00983:Drug metabolism - other enzymes)
A_22_P00004282	11.02	10.65	10.39	12.16	12.17	12.29	0.88	-0.19	down	0.00	yes	ref\|NR_104131\|ens\|ENST00000456551\|ens\|ENST00000452922\|linc\|lnc-CNN3-3:8	101928079	LINC01057	long intergenic non-protein coding RNA 1057	Homo sapiens long intergenic non-protein coding RNA 1057 (LINC01057), long non-coding RNA [NR_104131]	chr1	95123540	95123481
A_23_P370162	11	10.74	10.64	9.83	9.92	9.93	1.09	0.13	up	0.00	yes	ref\|NM_182969\|ref\|NM_001270381\|ref\|NM_001270380\|ens\|ENST00000531849	143570	XRRA1	X-ray radiation resistance associated 1	Homo sapiens X-ray radiation resistance associated 1 (XRRA1), transcript variant 1, mRNA [NM_182969]	chr11	74552650	74552591	GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0010165(response to X-ray)
A_23_P50697	9.85	9.52	10.12	8.02	8.39	8.12	1.20	0.27	up	0.00	yes	ref\|NM_006905\|ref\|NM_001297773\|ref\|NM_001184826\|ref\|NM_001184825	5669	PSG1	pregnancy specific beta-1-glycoprotein 1	Homo sapiens pregnancy specific beta-1-glycoprotein 1 (PSG1), transcript variant 1, mRNA [NM_006905]	chr19	43372365	43372306	GO:0005576(extracellular region);GO:0007565(female pregnancy)
A_21_P0004236	6.20	6.44	6.09	5.15	5.37	5.29	1.18	0.24	up	0.00	yes	linc\|lnc-C5orf17-1:2\|linc\|lnc-C5orf17-1:1\|linc\|TCONS_00009905\|linc\|TCONS_00009904		lnc-C5orf17-1	lnc-C5orf17-1:2	LNCipedia lincRNA (lnc-C5orf17-1), lincRNA [lnc-C5orf17-1:2]	chr5	24321155	24321214
A_33_P3363485	10.09	9.99	10.19	10.54	10.58	10.56	0.96	-0.07	down	0.00	yes	ref\|NM_018013\|ens\|ENST00000477448\|ens\|ENST00000618129\|ens\|ENST00000317357	55084	SOBP	sine oculis binding protein homolog (Drosophila)	Homo sapiens sine oculis binding protein homolog (Drosophila) (SOBP), mRNA [NM_018013]	chr6	107827569	107827628	GO:0007605(sensory perception of sound);GO:0007626(locomotory behavior);GO:0032184(SUMO polymer binding);GO:0042472(inner ear morphogenesis);GO:0046872(metal ion binding)
A_21_P0000812	5.92	5.87	5.72	6.36	6.50	6.40	0.91	-0.14	down	0.00	yes	ref\|NR_038458\|linc\|lnc-WFIKKN2-1:1\|gb\|AK123714\|tc\|THC2511559	400604	TOB1-AS1	TOB1 antisense RNA 1	Homo sapiens TOB1 antisense RNA 1 (TOB1-AS1), long non-coding RNA [NR_038458]	chr17	48945609	48945668
A_23_P139500	12.81	12.56	12.90	11	11.41	10.77	1.15	0.21	up	0.00	yes	ref\|NM_030762\|ens\|ENST00000242728\|gb\|AY665467\|gb\|BC025968	79365	BHLHE41	basic helix-loop-helix family, member e41	Homo sapiens basic helix-loop-helix family, member e41 (BHLHE41), mRNA [NM_030762]	chr12	26273691	26273632	GO:0000122(negative regulation of transcription from RNA polymerase II promoter);GO:0000978(RNA polymerase II core promoter proximal region sequence-specific DNA binding);GO:0001078(RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription);GO:0001102(RNA polymerase II activating transcription factor binding);GO:0001191(RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription);GO:0003705(RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity);GO:0003714(transcription corepressor activity);GO:0005515(protein binding);GO:0005634(nucleus);GO:0006366(transcription from RNA polymerase II promoter);GO:0007623(circadian rhythm);GO:0008283(cell proliferation);GO:0009887(organ morphogenesis);GO:0010832(negative regulation of myotube differentiation);GO:0010944(negative regulation of transcription by competitive promoter binding);GO:0030154(cell differentiation);GO:0032922(circadian regulation of gene expression);GO:0042803(protein homodimerization activity);GO:0042826(histone deacetylase binding);GO:0043425(bHLH transcription factor binding);GO:0043426(MRF binding);GO:0045892(negative regulation of transcription, DNA-dependent);GO:0046982(protein heterodimerization activity);GO:0070888(E-box binding)	04710(Circadian rhythm)
A_22_P00012354	5.20	5.38	5.42	6.27	6.20	6.55	0.84	-0.25	down	0.00	yes	linc\|lnc-PRDX6-1:1		lnc-PRDX6-1	lnc-PRDX6-1:1	LNCipedia lincRNA (lnc-PRDX6-1), lincRNA [lnc-PRDX6-1:1]	chr1	173572308	173572367
A_33_P3422233	9.24	9.14	8.85	9.99	10.11	10.04	0.90	-0.15	down	0.00	yes	ref\|NM_020894\|ens\|ENST00000389851\|ens\|ENST00000503548\|gb\|AB040963	57654	UVSSA	UV-stimulated scaffold protein A	Homo sapiens UV-stimulated scaffold protein A (UVSSA), mRNA [NM_020894]	chr4	1381673	1381732	GO:0000993(RNA polymerase II core binding);GO:0005515(protein binding);GO:0005694(chromosome);GO:0006283(transcription-coupled nucleotide-excision repair);GO:0009411(response to UV);GO:0016567(protein ubiquitination)
A_21_P0005503	10.24	10.18	10.14	9.61	9.36	9.31	1.08	0.11	up	0.00	yes	linc\|lnc-SBDS-2:2\|linc\|TCONS_00013856		lnc-SBDS-2	lnc-SBDS-2:2	LNCipedia lincRNA (lnc-SBDS-2), lincRNA [lnc-SBDS-2:2]	chr7	66798498	66798439
A_23_P40956	8.55	8.42	8.70	7.89	7.86	7.74	1.09	0.13	up	0.00	yes	ref\|NM_016362\|ref\|NM_001134941\|ref\|NM_001302821\|ref\|NM_001302822	51738	GHRL	ghrelin/obestatin prepropeptide	Homo sapiens ghrelin/obestatin prepropeptide (GHRL), transcript variant 1, mRNA [NM_016362]	chr3	10327552	10327493	GO:0000187(activation of MAPK activity);GO:0001664(G-protein coupled receptor binding);GO:0001696(gastric acid secretion);GO:0001937(negative regulation of endothelial cell proliferation);GO:0005576(extracellular region);GO:0005615(extracellular space);GO:0005788(endoplasmic reticulum lumen);GO:0006006(glucose metabolic process);GO:0007186(G-protein coupled receptor signaling pathway);GO:0007204(elevation of cytosolic calcium ion concentration);GO:0008154(actin polymerization or depolymerization);GO:0008343(adult feeding behavior);GO:0009725(response to hormone stimulus);GO:0009755(hormone-mediated signaling pathway);GO:0016358(dendrite development);GO:0016525(negative regulation of angiogenesis);GO:0016608(growth hormone-releasing hormone activity);GO:0030252(growth hormone secretion);GO:0030296(protein tyrosine kinase activator activity);GO:0030424(axon);GO:0031768(ghrelin receptor binding);GO:0032024(positive regulation of insulin secretion);GO:0032095(regulation of response to food);GO:0032100(positive regulation of appetite);GO:0032691(negative regulation of interleukin-1 beta production);GO:0034774(secretory granule lumen);GO:0040013(negative regulation of locomotion);GO:0040018(positive regulation of multicellular organism growth);GO:0042127(regulation of cell proliferation);GO:0042322(negative regulation of circadian sleep/wake cycle, REM sleep);GO:0042536(negative regulation of tumor necrosis factor biosynthetic process);GO:0043066(negative regulation of apoptotic process);GO:0043400(cortisol secretion);GO:0043627(response to estrogen stimulus);GO:0044267(cellular protein metabolic process);GO:0045409(negative regulation of interleukin-6 biosynthetic process);GO:0046010(positive regulation of circadian sleep/wake cycle, non-REM sleep);GO:0046676(negative regulation of insulin secretion);GO:0046697(decidualization);GO:0050728(negative regulation of inflammatory response);GO:0051216(cartilage development);GO:0051461(positive regulation of corticotropin secretion);GO:0051464(positive regulation of cortisol secretion);GO:0051965(positive regulation of synapse assembly);GO:0060079(regulation of excitatory postsynaptic membrane potential);GO:0060124(positive regulation of growth hormone secretion);GO:0060399(positive regulation of growth hormone receptor signaling pathway);GO:0061098(positive regulation of protein tyrosine kinase activity)	04024(cAMP signaling pathway\|04080:Neuroactive ligand-receptor interaction)

document location:

summary/3_mRNA_differential_expression/*vs*/1_Diff_Analysis/*vs*_diff.xlsx

3.3.2 Volcano of differentially expressed mRNA

By using the volcano can understand the overall distribution of differentially expressed genes. Log2(foldchange) as the abscissa, representing the gene in different samples of the fold change in the fold; -log10(pvalue) as the ordinate, representing the gene expression differences in the statistical significance. In the figure, red indicates significant up-regulated differentially expressed genes, blue indicates significantly down-regulated significantly differentially expressed genes, and gray spots represent non-significantly differentially expressed genes.

document location:

summary/3_mRNA_differential_expression/*vs*/1_Diff_Analysis/*vs*_diff_volcano.png

3.3.3 Heatmap of differentially expressed mRNA

Heatmap is a graphical representation of data where the individual z values (repeated) or Log10 (non-repeated) contained in a matrix are represented as color scheme. Calculation formula of z value is shown below. Sample-i means expression level(the value after normalization). In the figure, different colors represent different levels of gene expression, red indicates high expression genes and blue indicates low expression genes.

document location:

summary/3_mRNA_differential_expression/*vs*/1_Diff_Analysis/*vs*_diff_heatmap.png

3.3.4 GO enrichment analysis of differentially expressed genes

Gene ontology (GO)(http://www.geneontology.org) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis.

GO is part of a larger classification effort, the Open Biomedical Ontologies (OBO).

Although gene nomenclature itself aims to maintain and develop controlled vocabulary of gene and gene products, the Gene Ontology extends the effort by using markup language to make the data (not only of the genes and their products but also of all their attributes) machine readable, and to do so in a way that is unified across all species (whereas gene nomenclature conventions vary by biologic taxon).

Significant GO terms were calculated by Hypergeometric equation as shown below. TB gene number=number of total genes; TS gene number=number of differentially expressed genes in total genes; B gene number=total number of gene in all GO terms; S gene number=number of differentially expressed genes in this GO term. Those GO terms with p value<0.05 were defined as significant GO terms.

Significant GO terms:

GO_ID	GO_Term	GO_function	GO_class	S gene number	TS gene number	B gene number	TB gene number	pvalue
GO:0000786	nucleosome	cellular_component	12	33	1778	92	15922	3.95e-10
GO:0006271	DNA strand elongation involved in DNA replication	biological_process	11	13	1778	33	15922	2.66e-05
GO:0006334	nucleosome assembly	biological_process	12	27	1778	107	15922	3.42e-05
GO:0006298	mismatch repair	biological_process	10	12	1778	33	15922	0.00
GO:0000083	regulation of transcription involved in G1/S phase of mitotic cell cycle	biological_process	13	10	1778	25	15922	0.00
GO:0032201	telomere maintenance via semi-conservative replication	biological_process	11	10	1778	25	15922	0.00
GO:0006284	base-excision repair	biological_process	10	14	1778	45	15922	0.00
GO:0000723	telomere maintenance	biological_process	9	20	1778	80	15922	0.00
GO:0006281	DNA repair	biological_process	9	55	1778	317	15922	0.00
GO:0070182	DNA polymerase binding	molecular_function	6	5	1778	8	15922	0.00
GO:0000722	telomere maintenance via recombination	biological_process	10	10	1778	29	15922	0.00
GO:0007067	mitosis	biological_process	7	47	1778	268	15922	0.00
GO:0000278	mitotic cell cycle	biological_process	6	75	1778	476	15922	0.00
GO:0006260	DNA replication	biological_process	9	29	1778	145	15922	0.00
GO:0051461	positive regulation of corticotropin secretion	biological_process	12	3	1778	3	15922	0.00
GO:0032211	negative regulation of telomere maintenance via telomerase	biological_process	13	5	1778	9	15922	0.00
GO:0006270	DNA-dependent DNA replication initiation	biological_process	11	9	1778	27	15922	0.00
GO:0007044	cell-substrate junction assembly	biological_process	7	4	1778	6	15922	0.00
GO:0006285	base-excision repair, AP site formation	biological_process	9	5	1778	10	15922	0.00
GO:0022617	extracellular matrix disassembly	biological_process	6	24	1778	119	15922	0.00
GO:0051923	sulfation	biological_process	6	4	1778	7	15922	0.00
GO:0000777	condensed chromosome kinetochore	cellular_component	10	18	1778	83	15922	0.00
GO:0051539	4 iron, 4 sulfur cluster binding	molecular_function	6	11	1778	41	15922	0.00
GO:0006289	nucleotide-excision repair	biological_process	10	18	1778	84	15922	0.00
GO:0003697	single-stranded DNA binding	molecular_function	8	19	1778	91	15922	0.01
GO:0021784	postganglionic parasympathetic nervous system development	biological_process	9	3	1778	4	15922	0.01
GO:2000643	positive regulation of early endosome to late endosome transport	biological_process	5	3	1778	4	15922	0.01
GO:0031262	Ndc80 complex	cellular_component	10	3	1778	4	15922	0.01
GO:0045007	depurination	biological_process	10	3	1778	4	15922	0.01
GO:0005658	alpha DNA polymerase:primase complex	cellular_component	13	3	1778	4	15922	0.01
GO:0021615	glossopharyngeal nerve morphogenesis	biological_process	11	3	1778	4	15922	0.01
GO:0032369	negative regulation of lipid transport	biological_process	7	3	1778	4	15922	0.01
GO:0048010	vascular endothelial growth factor receptor signaling pathway	biological_process	10	22	1778	112	15922	0.01
GO:0051301	cell division	biological_process	5	55	1778	352	15922	0.01
GO:0046982	protein heterodimerization activity	molecular_function	6	63	1778	415	15922	0.01
GO:0017154	semaphorin receptor activity	molecular_function	6	5	1778	12	15922	0.01
GO:0071354	cellular response to interleukin-6	biological_process	8	4	1778	8	15922	0.01
GO:0031681	G-protein beta-subunit binding	molecular_function	5	4	1778	8	15922	0.01
GO:0031100	organ regeneration	biological_process	8	11	1778	44	15922	0.01
GO:0032793	positive regulation of CREB transcription factor activity	biological_process	14	6	1778	17	15922	0.01
GO:0048009	insulin-like growth factor receptor signaling pathway	biological_process	10	6	1778	17	15922	0.01
GO:0006297	nucleotide-excision repair, DNA gap filling	biological_process	11	7	1778	22	15922	0.01
GO:0005657	replication fork	cellular_component	11	7	1778	22	15922	0.01
GO:2000352	negative regulation of endothelial cell apoptotic process	biological_process	11	7	1778	22	15922	0.01
GO:0005814	centriole	cellular_component	10	19	1778	96	15922	0.01
GO:0006325	chromatin organization	biological_process	6	42	1778	261	15922	0.01
GO:0009165	nucleotide biosynthetic process	biological_process	9	5	1778	13	15922	0.01
GO:0033235	positive regulation of protein sumoylation	biological_process	12	5	1778	13	15922	0.01
GO:0006283	transcription-coupled nucleotide-excision repair	biological_process	11	13	1778	58	15922	0.01
GO:0000070	mitotic sister chromatid segregation	biological_process	8	7	1778	23	15922	0.01
GO:0006273	lagging strand elongation	biological_process	12	3	1778	5	15922	0.01
GO:0042799	histone methyltransferase activity (H4-K20 specific)	molecular_function	11	3	1778	5	15922	0.01
GO:0030911	TPR domain binding	molecular_function	6	3	1778	5	15922	0.01
GO:0018230	peptidyl-L-cysteine S-palmitoylation	biological_process	10	3	1778	5	15922	0.01
GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	biological_process	10	3	1778	5	15922	0.01
GO:0051414	response to cortisol stimulus	biological_process	9	3	1778	5	15922	0.01
GO:0072015	glomerular visceral epithelial cell development	biological_process	11	3	1778	5	15922	0.01
GO:0038033	positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway	biological_process	7	3	1778	5	15922	0.01
GO:0008484	sulfuric ester hydrolase activity	molecular_function	6	3	1778	5	15922	0.01
GO:0050702	interleukin-1 beta secretion	biological_process	9	3	1778	5	15922	0.01
GO:0071897	DNA biosynthetic process	biological_process	8	8	1778	29	15922	0.01
GO:0002116	semaphorin receptor complex	cellular_component	6	4	1778	9	15922	0.01
GO:0051147	regulation of muscle cell differentiation	biological_process	8	2	1778	2	15922	0.01
GO:0006272	leading strand elongation	biological_process	12	2	1778	2	15922	0.01
GO:0004832	valine-tRNA ligase activity	molecular_function	8	2	1778	2	15922	0.01
GO:0000727	double-strand break repair via break-induced replication	biological_process	12	2	1778	2	15922	0.01
GO:0072144	glomerular mesangial cell development	biological_process	10	2	1778	2	15922	0.01
GO:0008476	protein-tyrosine sulfotransferase activity	molecular_function	7	2	1778	2	15922	0.01
GO:0031508	centromeric heterochromatin assembly	biological_process	13	2	1778	2	15922	0.01
GO:0002086	diaphragm contraction	biological_process	11	2	1778	2	15922	0.01
GO:0006478	peptidyl-tyrosine sulfation	biological_process	8	2	1778	2	15922	0.01
GO:0034683	alphav-beta3 integrin complex	cellular_component	9	2	1778	2	15922	0.01
GO:0006438	valyl-tRNA aminoacylation	biological_process	13	2	1778	2	15922	0.01
GO:0050748	negative regulation of lipoprotein metabolic process	biological_process	7	2	1778	2	15922	0.01
GO:2000766	negative regulation of cytoplasmic translation	biological_process	10	2	1778	2	15922	0.01
GO:0042351	'de novo' GDP-L-fucose biosynthetic process	biological_process	12	2	1778	2	15922	0.01
GO:0090188	negative regulation of pancreatic juice secretion	biological_process	9	2	1778	2	15922	0.01
GO:0032226	positive regulation of synaptic transmission, dopaminergic	biological_process	11	2	1778	2	15922	0.01
GO:0021793	chemorepulsion of branchiomotor axon	biological_process	10	2	1778	2	15922	0.01
GO:0050923	regulation of negative chemotaxis	biological_process	6	2	1778	2	15922	0.01
GO:0046104	thymidine metabolic process	biological_process	11	2	1778	2	15922	0.01
GO:0032202	telomere assembly	biological_process	7	2	1778	2	15922	0.01
GO:0004797	thymidine kinase activity	molecular_function	10	2	1778	2	15922	0.01
GO:0006206	pyrimidine base metabolic process	biological_process	9	7	1778	24	15922	0.01
GO:0000790	nuclear chromatin	cellular_component	13	26	1778	149	15922	0.01
GO:0005178	integrin binding	molecular_function	6	20	1778	107	15922	0.01
GO:0001974	blood vessel remodeling	biological_process	6	9	1778	36	15922	0.02
GO:0010811	positive regulation of cell-substrate adhesion	biological_process	6	10	1778	42	15922	0.02
GO:0007160	cell-matrix adhesion	biological_process	6	18	1778	94	15922	0.02
GO:0000086	G2/M transition of mitotic cell cycle	biological_process	8	28	1778	165	15922	0.02
GO:0014065	phosphatidylinositol 3-kinase cascade	biological_process	10	7	1778	25	15922	0.02
GO:1900034	regulation of cellular response to heat	biological_process	7	9	1778	37	15922	0.02
GO:0045806	negative regulation of endocytosis	biological_process	7	4	1778	10	15922	0.02
GO:0001921	positive regulation of receptor recycling	biological_process	9	4	1778	10	15922	0.02
GO:0045792	negative regulation of cell size	biological_process	7	4	1778	10	15922	0.02
GO:0006081	cellular aldehyde metabolic process	biological_process	5	4	1778	10	15922	0.02
GO:0016572	histone phosphorylation	biological_process	9	4	1778	10	15922	0.02
GO:0030166	proteoglycan biosynthetic process	biological_process	8	4	1778	10	15922	0.02
GO:0034260	negative regulation of GTPase activity	biological_process	15	4	1778	10	15922	0.02

document location:

summary/3_mRNA_differential_expression/*vs*/2_GO_Enrichment/*vs*_GO_enrichment.txt

Barplot of enriched GO terms:

document location:

summary/3_mRNA_differential_expression/*vs*/2_GO_Enrichment/*vs*_GO_enrichment.png

Scatterplot of enriched GO terms:

Number of differentially expressed genes enriched in GO terms, p value and rich factor are shown in scatterplot. Rich factor=(number of differentially expressed genes in GO term)/(total number of genes in GO term). The larger rich factor is, the higher enrichment is.

document location:

summary/3_mRNA_differential_expression/*vs*/2_GO_Enrichment/*vs*_GO_enrichment_scatterplot.png

3.3.5 KEGG enrichment analysis of differentially expressed genes

KEGG (Kyoto Encyclopedia of Genes and Genomes) (http://www.kegg.jp/) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.

Significant KEGG pathways were calculated by Hypergeometric equation as shown below. TB gene number=number of total genes; TS gene number=number of differentially expressed genes in total genes; B gene number=total number of genes in KEGG pathways; S gene number=number of differentially expressed genes in this KEGG pathway. Those KEGG pathways with p value<0.05 were defined as significant KEGG pathways.

Significant KEGG pathways:

pathway_id	pathway_name	S gene number	TS gene number	B gene number	TB gene number	pvalue
ko05322	Systemic lupus erythematosus	13	713	30	5949	1.60e-05
ko03410	Base excision repair	9	713	26	5949	0.00
ko05203	Viral carcinogenesis	14	713	57	5949	0.01
ko05204	Chemical carcinogenesis	2	713	2	5949	0.01
ko03030	DNA replication	7	713	25	5949	0.02
ko04151	PI3K-Akt signaling pathway	19	713	102	5949	0.03
ko00052	Galactose metabolism\|04973:Carbohydrate digestion and absorption	4	713	13	5949	0.06
ko00500	Starch and sucrose metabolism	4	713	13	5949	0.06
ko00980	Metabolism of xenobiotics by cytochrome P450	3	713	8	5949	0.06
ko01212	Fatty acid metabolism\|01040:Biosynthesis of unsaturated fatty acids	10	713	50	5949	0.07
ko00240	Pyrimidine metabolism	7	713	31	5949	0.07
ko04142	Lysosome	13	713	70	5949	0.07
ko00480	Glutathione metabolism	6	713	28	5949	0.11
ko04071	Sphingolipid signaling pathway	4	713	16	5949	0.12
ko01220	Degradation of aromatic compounds\|00010:Glycolysis / Gluconeogenesis\|00040:Pentose and glucuronate interconversions\|00561:Glycerolipid metabolism	1	713	1	5949	0.12
ko00010	Glycolysis / Gluconeogenesis\|00620:Pyruvate metabolism\|00640:Propanoate metabolism\|00270:Cysteine and methionine metabolism\|04922:Glucagon signaling pathway	6	713	29	5949	0.13
ko04921	Oxytocin signaling pathway	3	713	11	5949	0.14
ko00531	Glycosaminoglycan degradation	4	713	17	5949	0.14
ko00760	Nicotinate and nicotinamide metabolism	4	713	17	5949	0.14
ko04114	Oocyte meiosis	4	713	17	5949	0.14
ko04974	Protein digestion and absorption	6	713	30	5949	0.14
ko00512	Mucin type O-glycan biosynthesis	5	713	24	5949	0.15
ko04510	Focal adhesion	2	713	6	5949	0.16
ko04122	Sulfur relay system	2	713	6	5949	0.16
ko04140	Regulation of autophagy	4	713	18	5949	0.16
ko00532	Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate	4	713	18	5949	0.16
ko00310	Lysine degradation	8	713	45	5949	0.16
ko00562	Inositol phosphate metabolism	11	713	67	5949	0.17
ko00600	Sphingolipid metabolism	7	713	40	5949	0.20
ko04911	Insulin secretion	3	713	13	5949	0.20
ko00250	Alanine, aspartate and glutamate metabolism	3	713	13	5949	0.20
ko04612	Antigen processing and presentation	3	713	13	5949	0.20
ko04623	Cytosolic DNA-sensing pathway	2	713	7	5949	0.20
ko03320	PPAR signaling pathway	4	713	20	5949	0.21
ko03440	Homologous recombination	4	713	20	5949	0.21
ko04141	Protein processing in endoplasmic reticulum	23	713	161	5949	0.21
ko05223	Non-small cell lung cancer	1	713	2	5949	0.23
ko04916	Melanogenesis	1	713	2	5949	0.23
ko00053	Ascorbate and aldarate metabolism\|00562:Inositol phosphate metabolism	1	713	2	5949	0.23
ko05012	Parkinson's disease	2	713	8	5949	0.25
ko03430	Mismatch repair	2	713	8	5949	0.25
ko03460	Fanconi anemia pathway	6	713	36	5949	0.26
ko04152	AMPK signaling pathway	5	713	29	5949	0.26
ko00910	Nitrogen metabolism	3	713	15	5949	0.26
ko00051	Fructose and mannose metabolism	3	713	15	5949	0.26
ko00514	Other types of O-glycan biosynthesis	4	713	22	5949	0.27
ko00130	Ubiquinone and other terpenoid-quinone biosynthesis	2	713	9	5949	0.29
ko00260	Glycine, serine and threonine metabolism	3	713	16	5949	0.30
ko04972	Pancreatic secretion	3	713	16	5949	0.30
ko02010	ABC transporters	7	713	46	5949	0.31
ko04360	Axon guidance	11	713	77	5949	0.31
ko00785	Lipoic acid metabolism	1	713	3	5949	0.32
ko04932	Non-alcoholic fatty liver disease (NAFLD)	1	713	3	5949	0.32
ko05169	Epstein-Barr virus infection	1	713	3	5949	0.32
ko04330	Notch signaling pathway	6	713	39	5949	0.32
ko00534	Glycosaminoglycan biosynthesis - heparan sulfate / heparin	3	713	17	5949	0.33
ko04970	Salivary secretion	3	713	18	5949	0.37
ko04110	Cell cycle	7	713	49	5949	0.37
ko04620	Toll-like receptor signaling pathway	2	713	11	5949	0.39
ko00630	Glyoxylate and dicarboxylate metabolism	2	713	11	5949	0.39
ko00511	Other glycan degradation	2	713	11	5949	0.39
ko03018	RNA degradation	8	713	58	5949	0.39
ko00603	Glycosphingolipid biosynthesis - globo series	1	713	4	5949	0.40
ko04940	Type I diabetes mellitus	1	713	4	5949	0.40
ko04270	Vascular smooth muscle contraction	2	713	12	5949	0.43
ko05110	Vibrio cholerae infection	1	713	5	5949	0.47
ko04973	Carbohydrate digestion and absorption	1	713	5	5949	0.47
ko01210	2-Oxocarboxylic acid metabolism\|01230:Biosynthesis of amino acids\|00330:Arginine and proline metabolism	1	713	5	5949	0.47
ko00071	Fatty acid degradation	1	713	5	5949	0.47
ko00970	Aminoacyl-tRNA biosynthesis	5	713	38	5949	0.49
ko04014	Ras signaling pathway	26	713	214	5949	0.50
ko00790	Folate biosynthesis	2	713	14	5949	0.51
ko04962	Vasopressin-regulated water reabsorption	2	713	14	5949	0.51
ko04975	Fat digestion and absorption	1	713	6	5949	0.54
ko04723	Retrograde endocannabinoid signaling	1	713	6	5949	0.54
ko00750	Vitamin B6 metabolism	1	713	6	5949	0.54
ko05132	Salmonella infection	1	713	6	5949	0.54
ko03008	Ribosome biogenesis in eukaryotes	8	713	66	5949	0.54
ko00561	Glycerolipid metabolism	6	713	49	5949	0.54
ko00040	Pentose and glucuronate interconversions	2	713	15	5949	0.55
ko04146	Peroxisome	5	713	41	5949	0.56
ko05206	MicroRNAs in cancer	4	713	33	5949	0.57
ko05014	Amyotrophic lateral sclerosis (ALS)	1	713	7	5949	0.59
ko04550	Signaling pathways regulating pluripotency of stem cells	4	713	34	5949	0.59
ko05166	HTLV-I infection	2	713	17	5949	0.62
ko04742	Taste transduction	2	713	17	5949	0.62
ko00604	Glycosphingolipid biosynthesis - ganglio series	1	713	8	5949	0.64
ko04919	Thyroid hormone signaling pathway	3	713	27	5949	0.64
ko04020	Calcium signaling pathway	11	713	99	5949	0.65
ko00280	Valine, leucine and isoleucine degradation	2	713	18	5949	0.65
ko05202	Transcriptional misregulation in cancers	10	713	91	5949	0.66
ko04015	Rap1 signaling pathway	10	713	92	5949	0.68
ko00860	Porphyrin and chlorophyll metabolism	2	713	19	5949	0.68
ko00450	Selenocompound metabolism	1	713	9	5949	0.68
ko05162	Measles	1	713	9	5949	0.68
ko00670	One carbon pool by folate	1	713	9	5949	0.68
ko00140	Steroid hormone biosynthesis	3	713	30	5949	0.72
ko04144	Endocytosis	15	713	140	5949	0.72
ko00920	Sulfur metabolism	1	713	10	5949	0.72

document location:

summary/3_mRNA_differential_expression/*vs*/3_KEGG_Enrichment/*vs*_KEGG_enrichment.txt

Scatterplot of enriched KEGG pathways:

Number of differentially expressed genes enriched in KEGG pathway, p value and rich factor are shown in scatterplot. Rich factor=(number of differentially expressed genes in KEGG pathway)/(total number of genes in KEGG pathway). The larger rich factor is, the higher enrichment is.

document location:

summary/3_mRNA_differential_expression/*vs*/3_KEGG_Enrichment/*vs*_KEGG_enrichment_scatterplot.png

KEGG pathway maps:

Graphical map objects

The KEGG pathway map is a moleculalr interaction/reaction network diagram represented in terms of the KEGG Orthology (KO) groups, so that experimental evidence in specific organisms can be generalized to other organisms through genomic information. Each map is manually drawn with in-house software called KegSketch, which generates the KGML+ file. This file is an SVG file containing graphics objects that are associated with KEGG objects (see KEGG object identifiers). Basic graphics objects in the reference KEGG pathway maps are:

boxes - ortholog (KO) groups identified by K numbers and, in metabolic maps, reactions identified by R numbers as well

circles - other molecules, usually chemical compounds identified by C numbers, but including glycans identified by G numbers

lines - reactions identified by R numbers in metabolic maps; ortholog (KO) groups identified by K numbers in global metabolism maps

and in organism specific pathway maps that are computationally generated:

boxes - genes or gene products identified by the combination of the KEGG organism code and gene identifiers

These map objects can be searched in the search box at the top of the KEGG PATHWAY page, in the search box in each pathway map, and by the KEGG Mapper tools.

Convention of map number prefix

Each pathway map is identified by the combination of 2-4 letter code and 5 digit number (see KEGG Identifiers). The prefix has the following meaning:

map - Reference pathway

ko - Reference pathway (KO)

ec - Reference pathway (EC)

rn - Reference pathway (Reaction)

org - Organism-specific pathway map

Only the first reference pathway map is manually drawn; all other maps are computationally generated. For metabolic pathways, each box (or line) in the reference map is linked to the K number (KO identifeir), the EC number, and the R number (reaction identifier). The KO, EC, and reaction maps are linked to only one of them. For all metabolic and non-metabolic maps, K numbers are converted to gene identifiers in each organism to generate organism-specific pathways.

As shown above, "map" pathways are not colored, "ko/ec/rn" pathways are colored blue, and organism-specific pathways are colored green, where coloring indicates that map objects exist and are linked to corresponding entries. For global metabolism maps, "map" pathways are fully colored, so that "ko/ec/rn" pathways and organism-specific pathways are generated by reducing the coloring indicating the absence of corresponding entries.

In this study,all KEGG pathway maps were deposited in summary/3_mRNA_differential_expression/*vs*/3_KEGG_Enrichment/pathway_pics/

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