Agilent Gene Expression Microarray Report



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SalespersonKyle Navel
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1. Project information


1.1 Sample information


Species name: Human

Latin name: Homo sapiens

Specimens: tissue


1.2 Group information


SampleIDspeciescond1
Control_1hsaControl
Control_2hsaControl
Control_3hsaControl
Treatment_1hsaTreatment
Treatment_2hsaTreatment
Treatment_3hsaTreatment

1.3 Database


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

1.4 Bioinformatics software


Analysis item Software Version/date
Data normalizationGenespring14.8
GO and KEGG enrichment analysisPerl scripts in houseNA
Drawing toolsR,cytoacape3.3.0,3.5.1



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



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.


ProbeNameControl_1_NormSignalControl_2_NormSignalControl_3_NormSignalTreatment_1_NormSignalTreatment_2_NormSignalTreatment_3_NormSignalTreatment_3_flagsControl_3_flagsTreatment_2_flagsControl_1_flagsTreatment_1_flagsControl_2_flagsPrimaryAccessionRefSeqAccessionGenbankAccessionUniGeneIDEntrezGeneIDGeneSymbolGeneNameEnsemblIDDescriptionchrstartend
GE_BrightCorner18.5018.3518.2318.3718.3618.13DetectedDetectedDetectedDetectedDetectedDetected
DarkCorner3.533.343.953.443.293.48Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detected
A_21_P00143866.256.907.247.476.577.05DetectedDetectedDetectedNot DetectedDetectedDetected
A_33_P33968728.268.667.938.898.869.00DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001105533|gb|AK025639|gb|BC030538|tc|THC2601673NM_001105533NM_001105533Hs.18965279974CPED1cadherin-like and PC-esterase domain containing 1Homo sapiens cadherin-like and PC-esterase domain containing 1 (CPED1), transcript variant 2, mRNA [NM_001105533]chr7120901888120901947
A_33_P32677609.399.869.299.309.4510.38DetectedDetectedDetectedDetectedDetectedDetectedens|ENST0000037846354880BCORBCL6 corepressorENST00000378463BCL6 corepressor [Source:HGNC Symbol;Acc:HGNC:20893] [ENST00000378463]chrX3990912839909069
A_32_P19426410.1411.9811.7410.2411.3110.00DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001008708|ens|ENST00000295304|gb|HQ447717|gb|BC017941NM_001008708NM_001008708Hs.585944494143CHAC2ChaC, cation transport regulator homolog 2 (E. coli)ENST00000295304Homo sapiens ChaC, cation transport regulator homolog 2 (E. coli) (CHAC2), mRNA [NM_001008708]chr25400145454001513
A_23_P15374510.9912.2210.1311.2811.0411.74DetectedDetectedDetectedDetectedDetectedDetectedref|NM_006332|ens|ENST00000593731|ens|ENST00000600463|ens|ENST00000407280NM_006332NM_006332Hs.1462310437IFI30interferon, gamma-inducible protein 30ENST00000593731Homo sapiens interferon, gamma-inducible protein 30 (IFI30), mRNA [NM_006332]chr191828884018288899
A_33_P33528379.799.359.419.419.479.64DetectedDetectedDetectedDetectedDetectedDetectedchr2171521262171521203
A_21_P00112605.537.147.005.456.486.82DetectedDetectedDetectedNot DetectedNot DetectedDetectedens|ENST00000618272|linc|TCONS_l2_00007928|gb|BI821606|tc|THC2662262Hs.592320ENST00000618272603036639F1 NIH_MGC_115 Homo sapiens cDNA clone IMAGE:5177672 5', mRNA sequence [BI821606]chr14103675125103675184
A_33_P32358163.924.313.933.633.263.53Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedens|ENST00000436258|gb|BX647611|tc|THC2646539BX647611Hs.594815ENST00000436258DPY19L2 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:22305] [ENST00000436258]chr73512951635129457
A_21_P00141809.559.8610.209.569.7510.53DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000474396|tc|THC2637218XM_006715643XM_006715643115330GPR146G protein-coupled receptor 146ENST00000474396G protein-coupled receptor 146 [Source:HGNC Symbol;Acc:HGNC:21718] [ENST00000474396]chr710958411095900
A_24_P9449919.6910.7610.689.9710.0010.36DetectedDetectedDetectedDetectedDetectedDetectedref|NM_173829|ens|ENST00000513458|gb|BC127085|gb|BC127086NM_173829NM_173829Hs.69504285672SREK1IP1SREK1-interacting protein 1ENST00000513458Homo sapiens SREK1-interacting protein 1 (SREK1IP1), mRNA [NM_173829]chr56401894664018887
A_21_P00065073.895.224.806.094.705.51Not DetectedNot DetectedNot DetectedNot DetectedDetectedNot Detectedlinc|lnc-ARMCX4-1:1|linc|TCONS_00017209lnc-ARMCX4-1lnc-ARMCX4-1:1LNCipedia lincRNA (lnc-ARMCX4-1), lincRNA [lnc-ARMCX4-1:1]chrX100672726100672785
A_23_P20870611.1311.8411.7111.3311.7311.56DetectedDetectedDetectedDetectedDetectedDetectedref|NM_138764|ref|NM_001291428|ref|NM_001291431|ref|NM_138761NM_138764NM_138764Hs.624291581BAXBCL2-associated X proteinENST00000513545Homo sapiens BCL2-associated X protein (BAX), transcript variant sigma, mRNA [NM_138764]chr194946490449464963
A_33_P33888064.193.443.633.614.383.47Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedref|NM_001199327|gb|BC032865|ens|ENST00000370899|tc|THC2476487NM_001199327NM_001199327Hs.480085100526835FPGT-TNNI3KFPGT-TNNI3K readthroughENST00000370899Homo sapiens FPGT-TNNI3K readthrough (FPGT-TNNI3K), transcript variant 2, mRNA [NM_001199327]chr17493051574930574
A_33_P332483911.3211.2211.4211.8111.3311.71DetectedDetectedDetectedDetectedDetectedDetectedref|NM_006772|ens|ENST00000418600|ens|ENST00000455687|gb|AL713634NM_006772NM_006772Hs.5862648831SYNGAP1synaptic Ras GTPase activating protein 1ENST00000418600Homo sapiens synaptic Ras GTPase activating protein 1 (SYNGAP1), mRNA [NM_006772]chr63342055933420618
A_24_P3334949.5410.9510.8410.3910.7610.82DetectedDetectedDetectedDetectedDetectedDetectedref|NM_018994|ens|ENST00000375592|ref|XM_006710698|gb|BC006174NM_018994NM_018994Hs.52238454455FBXO42F-box protein 42ENST00000375592Homo sapiens F-box protein 42 (FBXO42), mRNA [NM_018994]chr11657719816577139
A_22_P000062747.657.417.767.846.988.85DetectedDetectedDetectedDetectedDetectedDetectedref|NR_109772|ens|ENST00000413050|ens|ENST00000437181|linc|lnc-FAM75D1-1:3NR_109772NR_109772Hs.528628101927502LOC101927502uncharacterized LOC101927502ENST00000413050Homo sapiens uncharacterized LOC101927502 (LOC101927502), long non-coding RNA [NR_109772]chr98436293084362989
A_23_P16161512.2812.8612.9811.7211.9611.47DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000534785|ens|ENST00000527618|ens|ENST00000527850|gb|AK307831AK307831Hs.20189723649POLA2polymerase (DNA directed), alpha 2, accessory subunitENST00000534785polymerase (DNA directed), alpha 2, accessory subunit [Source:HGNC Symbol;Acc:HGNC:30073] [ENST00000534785]chr116506211165063057
A_33_P33849589.469.239.439.479.499.36DetectedDetectedDetectedDetectedDetectedDetectedref|NM_014839|ref|NM_001166252|ens|ENST00000457765|ens|ENST00000370185NM_014839NM_014839Hs.132459890LPPR4lipid phosphate phosphatase-related protein type 4ENST00000457765Homo sapiens lipid phosphate phosphatase-related protein type 4 (LPPR4), transcript variant 1, mRNA [NM_014839]chr19977163299771691
A_22_P000189556.545.825.334.794.345.27Not DetectedNot DetectedNot DetectedDetectedNot DetectedDetectedlinc|lnc-SOX11-1:1|gb|BX089860|tc|THC2729651BX089860Hs.597532lnc-SOX11-1lnc-SOX11-1:1BX089860 NCI_CGAP_Brn23 Homo sapiens cDNA clone IMAGp998P014327 ; IMAGE:1704048, mRNA sequence [BX089860]chr258477325847791
A_22_P000095476.453.393.523.573.273.39Not DetectedNot DetectedNot DetectedDetectedNot DetectedNot Detectedref|NR_126414|linc|lnc-MAP2K6-3:1|gb|CB960713|tc|THC2717445NR_126414NR_126414Hs.569827104355297ABCA9-AS1ABCA9 antisense RNA 1Homo sapiens ABCA9 antisense RNA 1 (ABCA9-AS1), long non-coding RNA [NR_126414]chr176700818567008244
A_23_P21833110.5311.4510.8811.7011.3011.95DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001017916|ref|NM_001017917|ref|NM_001915|ens|ENST00000581573NM_001017916NM_001017916Hs.3552641534CYB561cytochrome b561ENST00000581573Homo sapiens cytochrome b561 (CYB561), transcript variant 2, mRNA [NM_001017916]chr176151068761510628
A_33_P645578613.9014.3014.2614.6014.4914.32DetectedDetectedDetectedDetectedDetectedDetectedref|NM_058172|ref|NM_001286781|ref|NM_001286780|ens|ENST00000403729NM_058172NM_058172Hs.162963118429ANTXR2anthrax toxin receptor 2ENST00000403729Homo sapiens anthrax toxin receptor 2 (ANTXR2), transcript variant 1, mRNA [NM_058172]chr48082287980822820
A_21_P00087058.688.208.849.028.938.84DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-POTEB-5:4|linc|lnc-POTEB-5:2|linc|TCONS_00023574|linc|TCONS_00023573lnc-POTEB-5lnc-POTEB-5:4LNCipedia lincRNA (lnc-POTEB-5), lincRNA [lnc-POTEB-5:4]chr152254161522541556
A_22_P000165263.733.363.473.553.273.35Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedens|ENST00000547094|linc|lnc-TMTC3-4:1|linc|lnc-TMTC3-4:2|linc|TCONS_00020510Hs.148998ENST00000547094chr129034340790343466
A_33_P32352073.724.503.454.235.523.34Not DetectedNot DetectedDetectedNot DetectedNot DetectedNot Detectedref|NM_018018|ref|NM_001143824|ens|ENST00000547477|ens|ENST00000266579NM_018018NM_018018Hs.44607755089SLC38A4solute carrier family 38, member 4ENST00000547477Homo sapiens solute carrier family 38, member 4 (SLC38A4), transcript variant 1, mRNA [NM_018018]chr124717362747173568
A_33_P333099115.1314.7214.4714.6914.5314.87DetectedDetectedDetectedDetectedDetectedDetectedref|XR_248772|gb|AK128451|tc|NP850545XR_248772XR_248772Hs.199368100134237LOC100134237uncharacterized LOC100134237PREDICTED: Homo sapiens uncharacterized LOC100134237 (LOC100134237), misc_RNA [XR_248772]chr13201215232012211
A_33_P33742999.439.019.129.479.2810.14DetectedDetectedDetectedDetectedDetectedDetectedref|NM_173561|ens|ENST00000373164|ens|ENST00000470102|ens|ENST00000244565NM_173561NM_173561Hs.158357222643UNC5CLunc-5 homolog C (C. elegans)-likeENST00000373164Homo sapiens unc-5 homolog C (C. elegans)-like (UNC5CL), mRNA [NM_173561]chr64099822240998163
A_33_P327470114.0513.3713.3413.5314.7513.17DetectedDetectedDetectedDetectedDetectedDetectedgb|AK024162|tc|THC2483964AK024162Homo sapiens cDNA FLJ14100 fis, clone MAMMA1000855. [AK024162]chr121445622144503
A_23_P8343610.4510.4310.6811.3210.5511.21DetectedDetectedDetectedDetectedDetectedDetectedref|NM_000285|ref|NM_001166056|ref|NM_001166057|ens|ENST00000591968NM_000285NM_000285Hs.364735184PEPDpeptidase DENST00000591968Homo sapiens peptidase D (PEPD), transcript variant 1, mRNA [NM_000285]chr193387799533877936
A_33_P32431388.498.769.018.429.038.56DetectedDetectedDetectedDetectedDetectedDetectedref|NM_182704|ens|ENST00000600586|ens|ENST00000335426|ens|ENST00000622070NM_182704NM_182704Hs.319284348303SELVselenoprotein VENST00000600586Homo sapiens selenoprotein V (SELV), mRNA [NM_182704]chr194000972940009788
A_22_P000080185.745.455.605.766.396.46DetectedNot DetectedDetectedNot DetectedNot DetectedNot Detectedens|ENST00000579045|linc|lnc-IFT20-3:1|gb|BC082966|tc|THC2513242BC082966Hs.20588ENST00000579045Homo sapiens cDNA clone IMAGE:6341252. [BC082966]chr172657422226574163
A_22_P000039373.633.333.363.493.263.28Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedens|ENST00000569945|linc|lnc-CGNL1-1:1|gb|BX641062|tc|THC2709601BX641062Hs.711270145781GCOM1GRINL1A complex locus 1ENST00000569945GRINL1A complex locus 1 [Source:HGNC Symbol;Acc:HGNC:26424] [ENST00000569945]chr155798482357984882
ERCC-00109_1206.987.226.817.327.047.70DetectedDetectedDetectedDetectedDetectedDetectedDQ854998
A_33_P32935938.077.967.988.577.498.06DetectedDetectedDetectedDetectedDetectedDetectedref|NM_152479|ens|ENST00000311308|ens|ENST00000593586|gb|BC029539NM_152479NM_152479Hs.631572148014TTC9Btetratricopeptide repeat domain 9BENST00000311308Homo sapiens tetratricopeptide repeat domain 9B (TTC9B), mRNA [NM_152479]chr194072202540721966
A_22_P000083893.993.976.004.815.665.55Not DetectedDetectedDetectedNot DetectedNot DetectedNot Detectedref|NM_001145545|ens|ENST00000505035|ens|ENST00000418886|linc|lnc-JMJD5-1:1NM_001145545NM_001145545Hs.120831162083C16orf82chromosome 16 open reading frame 82ENST00000505035Homo sapiens chromosome 16 open reading frame 82 (C16orf82), mRNA [NM_001145545]chr162708004827080107
A_21_P00122086.559.309.037.278.377.60DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-C21orf58-1:1|linc|TCONS_l2_00017315|linc|TCONS_l2_00017538|gb|AK127572Hs.596577lnc-C21orf58-1lnc-C21orf58-1:1Homo sapiens cDNA FLJ45665 fis, clone CTONG2027959. [AK127572]chr214787523447875175
A_23_P1010847.486.957.016.707.387.07DetectedDetectedDetectedDetectedDetectedDetectedref|NM_032598|ref|NM_001170698|ref|NM_001170697|ref|NM_001170695NM_032598NM_032598Hs.35106884690SPATA22spermatogenesis associated 22ENST00000573128Homo sapiens spermatogenesis associated 22 (SPATA22), transcript variant 2, mRNA [NM_032598]chr1733465553346496
A_23_P16212013.6014.0013.5113.5613.6113.42DetectedDetectedDetectedDetectedDetectedDetectedref|NM_006185|ref|NM_001286561|ref|NR_104476|ens|ENST00000616538NM_006185NM_006185Hs.3259784926NUMA1nuclear mitotic apparatus protein 1ENST00000616538Homo sapiens nuclear mitotic apparatus protein 1 (NUMA1), transcript variant 1, mRNA [NM_006185]chr117171530271715118
A_24_P29142610.1910.6610.7910.6810.3010.49DetectedDetectedDetectedDetectedDetectedDetectedref|NM_016316|ref|NM_001037872|ens|ENST00000258428|ens|ENST00000393445NM_016316NM_016316Hs.44307751455REV1REV1, polymerase (DNA directed)ENST00000258428Homo sapiens REV1, polymerase (DNA directed) (REV1), transcript variant 1, mRNA [NM_016316]chr2100019124100018768
A_32_P993116.036.976.267.647.186.18DetectedDetectedDetectedDetectedDetectedDetectedref|NM_181756|ref|NM_001207005|ens|ENST00000391958|gb|AK055310NM_181756NM_181756Hs.466891353355ZNF233zinc finger protein 233ENST00000391958Homo sapiens zinc finger protein 233 (ZNF233), transcript variant 1, mRNA [NM_181756]chr194477906044779119
A_21_P00114096.988.698.198.098.088.66DetectedDetectedDetectedDetectedDetectedDetectedlinc|TCONS_l2_00009502|gb|AK125393|tc|THC2508977Hs.586876XLOC_l2_004898BROAD Institute lincRNA (XLOC_l2_004898), lincRNA [TCONS_l2_00009502]chr154098343440983375
A_24_P1986299.399.689.369.739.4510.15DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001040616|ens|ENST00000559169|ref|XM_005254941|ref|XM_005254943NM_001040616NM_001040616Hs.10563355180LINSlines homolog (Drosophila)ENST00000559169Homo sapiens lines homolog (Drosophila) (LINS), mRNA [NM_001040616]chr15101109837101109778
A_19_P003229259.599.129.019.479.939.94DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000607519|ens|ENST00000606884|linc|lnc-WRNIP1-2:31|linc|lnc-WRNIP1-2:32Hs.188825ENST00000607519GMDS antisense RNA 1 (head to head) [Source:HGNC Symbol;Acc:HGNC:48993] [ENST00000607519]chr624811892481248
A_22_P000251885.263.883.276.104.985.05Not DetectedNot DetectedNot DetectedNot DetectedDetectedNot Detectedens|ENST00000512831|linc|lnc-NPY5R-2:1|linc|TCONS_00007672|tc|THC2642096ENST00000512831Q6NT14_HUMAN (Q6NT14) ZNF80 protein (Fragment), partial (13%) [THC2642096]chr4163662989163663048
A_23_P5261010.7711.0711.0610.009.559.54DetectedDetectedDetectedDetectedDetectedDetectedref|NM_000107|ref|NM_001300734|ens|ENST00000378601|ens|ENST00000617847NM_000107NM_000107Hs.7003381643DDB2damage-specific DNA binding protein 2, 48kDaENST00000378601Homo sapiens damage-specific DNA binding protein 2, 48kDa (DDB2), mRNA [NM_000107]chr114726062347260682
A_22_P000046223.494.655.304.993.454.60Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedlinc|lnc-CST7-2:1lnc-CST7-2lnc-CST7-2:1LNCipedia lincRNA (lnc-CST7-2), lincRNA [lnc-CST7-2:1]chr202499844024998499
A_23_P281410.4910.139.9010.939.7710.55DetectedDetectedDetectedDetectedDetectedDetectedref|NM_005905|ref|NM_001127217|ens|ENST00000379826|ens|ENST00000350148NM_005905NM_005905Hs.1231194093SMAD9SMAD family member 9ENST00000379826Homo sapiens SMAD family member 9 (SMAD9), transcript variant b, mRNA [NM_005905]chr133742287237422813
A_23_P14060212.9013.4912.8513.1713.1113.29DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001033088|ref|NR_028052|ens|ENST00000561573|gb|AK312641NM_001033088NM_001033088Hs.13547151335NGRNneugrin, neurite outgrowth associatedENST00000561573Homo sapiens neugrin, neurite outgrowth associated (NGRN), transcript variant 2, mRNA [NM_001033088]chr159081447390814532
A_33_P327611212.9212.7912.1912.4713.5911.70DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-CTD-2517M22.14.1-1:3|linc|lnc-CTD-2517M22.14.1-1:4|gb|AK126743|tc|THC2487449AK126743Hs.521937lnc-CTD-2517M22.14.1-1lnc-CTD-2517M22.14.1-1:3Homo sapiens cDNA FLJ44789 fis, clone BRACE3038760. [AK126743]chr8145722802145722743
A_21_P00128967.807.779.108.138.447.96DetectedDetectedDetectedDetectedDetectedDetectedlinc|TCONS_l2_00022830|tc|THC2775530XLOC_l2_011987BROAD Institute lincRNA (XLOC_l2_011987), lincRNA [TCONS_l2_00022830]chr53412429034124231
A_22_P000103797.628.018.477.508.038.11DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-MYL12A-1:1|gb|AK093324|tc|THC2533948AK093324Hs.589563lnc-MYL12A-1lnc-MYL12A-1:1Homo sapiens cDNA FLJ36005 fis, clone TESTI2015350. [AK093324]chr1832471113247170
A_23_P21093913.5115.0414.5114.5614.4514.64DetectedDetectedDetectedDetectedDetectedDetectedref|NM_181468|ref|NM_002212|ref|NM_181466|ref|NM_001267810NM_181468NM_181468Hs.7439923692EIF6eukaryotic translation initiation factor 6ENST00000374450Homo sapiens eukaryotic translation initiation factor 6 (EIF6), transcript variant 2, mRNA [NM_181468]chr203386699833866939
A_24_P3490398.6710.6110.319.0910.269.63DetectedDetectedDetectedDetectedDetectedDetectedref|NM_020754|ens|ENST00000264245|ref|XM_006713714|ref|XM_005247671NM_020754NM_020754Hs.66821857514ARHGAP31Rho GTPase activating protein 31ENST00000264245Homo sapiens Rho GTPase activating protein 31 (ARHGAP31), mRNA [NM_020754]chr3119136009119136068
A_24_P14368611.4112.4812.7812.3511.8711.94DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001080394|ref|NM_001282919|ref|NM_001282916|ref|NR_104581NM_001080394NM_001080394Hs.38105823514SPIDRscaffolding protein involved in DNA repairENST00000297423Homo sapiens scaffolding protein involved in DNA repair (SPIDR), transcript variant 1, mRNA [NM_001080394]chr84864202748647927
A_23_P11534612.0612.2512.5211.9311.0711.77DetectedDetectedDetectedDetectedDetectedDetectedref|NM_006893|ref|NM_001201478|ens|ENST00000468891|ens|ENST00000484492NM_006893NM_006893Hs.4975811939EIF2Deukaryotic translation initiation factor 2DENST00000468891Homo sapiens eukaryotic translation initiation factor 2D (EIF2D), transcript variant 1, mRNA [NM_006893]chr1206770531206770472
A_22_P000105906.583.234.985.134.073.99Not DetectedNot DetectedNot DetectedDetectedNot DetectedNot Detectedens|ENST00000553534|linc|lnc-NDRG2-3:1ENST00000553534chr142140432321404264
A_22_P0001489216.1716.1715.7015.8516.1915.65DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000521326|linc|lnc-SLC7A13-1:2|linc|lnc-SLC7A13-1:1|gb|BC038731BC038731Hs.561806ENST00000521326Homo sapiens cDNA clone IMAGE:5267578. [BC038731]chr88735537087355311
A_21_P00141483.363.233.203.303.213.15Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedgb|XR_108599XR_108599Hs.570950PREDICTED: Homo sapiens uncharacterized LOC100506329 (LOC100506329), misc_RNA [XR_108599]chr55075793350757992
A_21_P001225911.5111.7211.8811.0912.9710.38DetectedDetectedCompromisedCompromisedDetectedDetectedlinc|TCONS_l2_00017650|linc|TCONS_l2_00017653XLOC_l2_009328BROAD Institute lincRNA (XLOC_l2_009328), lincRNA [TCONS_l2_00017650]chr222466300124663060
A_33_P32373933.353.223.193.293.203.14Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedref|NM_001300778|ref|NM_003440|ref|NM_001300777|ref|NM_001300776NM_001300778NM_001300778Hs.1815527699ZNF140zinc finger protein 140Homo sapiens zinc finger protein 140 (ZNF140), transcript variant 4, mRNA [NM_001300778]chr12133684178133684237
A_23_P2514866.937.306.616.576.476.79DetectedDetectedDetectedDetectedDetectedDetectedref|NM_006438|gb|AB002631|tc|THC2478678NM_006438NM_006438Hs.17661510584COLEC10collectin sub-family member 10 (C-type lectin)Homo sapiens collectin sub-family member 10 (C-type lectin) (COLEC10), mRNA [NM_006438]chr8120118876120118935
A_33_P32278807.918.148.018.406.768.23DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001197247|ref|NM_001145009|ens|ENST00000396948|ens|ENST00000425234NM_001197247NM_001197247Hs.37604611118BTN3A2butyrophilin, subfamily 3, member A2ENST00000396948Homo sapiens butyrophilin, subfamily 3, member A2 (BTN3A2), transcript variant 3, mRNA [NM_001197247]chr62637598526376044
A_33_P326730511.4212.0611.7711.9411.2712.00DetectedDetectedDetectedDetectedDetectedDetectedref|NM_173595|ens|ENST00000267116|ens|ENST00000548241|gb|AK056831NM_173595NM_173595Hs.524506283373ANKRD52ankyrin repeat domain 52ENST00000267116Homo sapiens ankyrin repeat domain 52 (ANKRD52), mRNA [NM_173595]chr125663165056631591
A_22_P000175133.876.425.665.775.075.42Not DetectedNot DetectedNot DetectedNot DetectedDetectedDetectedlinc|lnc-WDFY2-1:1|tc|THC2661765|tc|THC2604700lnc-WDFY2-1lnc-WDFY2-1:1Q9BSH2_HUMAN (Q9BSH2) MARVELD3 protein (Fragment), partial (10%) [THC2604700]chr135237881352378872
A_21_P00057684.935.366.493.293.623.13Not DetectedDetectedNot DetectedNot DetectedNot DetectedNot Detectedref|NR_126028|ens|ENST00000519500|linc|lnc-KHDRBS3-4:4|linc|lnc-KHDRBS3-4:6NR_126028NR_126028552853NCRNA00250non-protein coding RNA 250ENST00000519500Homo sapiens non-protein coding RNA 250 (NCRNA00250), long non-coding RNA [NR_126028]chr8135854504135854698
A_21_P00132379.528.868.909.409.319.09DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-VKORC1L1-2:1|linc|TCONS_l2_00025988lnc-VKORC1L1-2lnc-VKORC1L1-2:1LNCipedia lincRNA (lnc-VKORC1L1-2), lincRNA [lnc-VKORC1L1-2:1]chr76600670766006766
A_21_P00030683.303.943.974.914.533.43Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedlinc|lnc-RP11-433C9.2.1-1:2|linc|TCONS_00006330lnc-RP11-433C9.2.1-1lnc-RP11-433C9.2.1-1:2LNCipedia lincRNA (lnc-RP11-433C9.2.1-1), lincRNA [lnc-RP11-433C9.2.1-1:2]chr3184119448184144427
A_33_P333364212.4111.7111.5112.1112.7111.32DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000399003|linc|lnc-MPEG1-1:1|gb|AK131315|tc|THC2487937AK131315Hs.533590ENST00000399003Homo sapiens cDNA FLJ16303 fis, clone PROST2019487. [AK131315]chr115903640859036349
A_24_P425573.283.193.163.253.193.12Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedref|NM_001018036|ref|NM_001142626|ens|ENST00000342443|ens|ENST00000554435NM_001018036NM_001018036Hs.1604117253TSHRthyroid stimulating hormone receptorENST00000342443Homo sapiens thyroid stimulating hormone receptor (TSHR), transcript variant 2, mRNA [NM_001018036]chr148155746481558910
A_21_P00142078.597.707.708.417.128.76DetectedDetectedDetectedDetectedDetectedDetectedref|XR_242321|ref|XR_250248|ref|XR_252275|tc|THC2645710XR_242321XR_242321101927721LOC101927721uncharacterized LOC101927721PREDICTED: Homo sapiens uncharacterized LOC101927721 (LOC101927721), ncRNA [XR_242321]chr7100944565100944624
A_22_P0002156513.4112.4812.7713.6012.6613.69DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000531523|linc|lnc-RNF151-1:1|tc|THC2732461677844SNORA78small nucleolar RNA, H/ACA box 78ENST00000531523small nucleolar RNA host gene 9 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:33102] [ENST00000531523]chr1620154512015510
A_21_P000010217.9317.8818.0318.0617.7218.01DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001190470|ens|ENST00000604882NM_001190470NM_001190470Hs.666077100462981MTRNR2L2MT-RNR2-like 2ENST00000604882Homo sapiens MT-RNR2-like 2 (MTRNR2L2), mRNA [NM_001190470]chr57994587879945819
A_24_P40109013.0111.0911.2212.3911.3711.78DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000442006ENST00000442006chr13917595439176015
A_21_P00032883.263.173.143.233.183.11Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedens|ENST00000479244|linc|lnc-VGLL3-2:1|linc|lnc-VGLL3-2:2|linc|TCONS_00007195ENST00000479244chr38631378886313729
A_24_P91462510.5310.8011.0210.7110.3110.51DetectedDetectedDetectedDetectedDetectedDetectedref|NM_207406|ref|NM_001159547|ens|ENST00000611697|ens|ENST00000504360NM_207406NM_207406Hs.120591389206BEND4BEN domain containing 4ENST00000611697Homo sapiens BEN domain containing 4 (BEND4), transcript variant 1, mRNA [NM_207406]chr44214579242145733
A_33_P33935435.996.346.986.816.335.87DetectedDetectedDetectedDetectedDetectedDetectedgb|AL831916AL831916Hs.590968400692LOC400692uncharacterized LOC400692Homo sapiens mRNA; cDNA DKFZp761D1918 (from clone DKFZp761D1918). [AL831916]chr193803648938036430
A_22_P000258568.428.438.038.527.878.30DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000414038|linc|lnc-HECA-2:1|linc|TCONS_l2_00024448|linc|TCONS_l2_00025257100132735LOC100132735uncharacterized LOC100132735ENST00000414038chr6140176043140176102
A_23_P105598.547.968.308.137.947.71DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001080395|ref|NM_004920|ens|ENST00000374792|ens|ENST00000570932NM_001080395NM_001080395Hs.5145759625AATKapoptosis-associated tyrosine kinaseENST00000374792Homo sapiens apoptosis-associated tyrosine kinase (AATK), transcript variant 1, mRNA [NM_001080395]chr177909125479091195
A_23_P10963610.6210.1510.1011.0410.7011.23DetectedDetectedDetectedDetectedDetectedDetectedref|NM_015541|ens|ENST00000496559|ens|ENST00000383703|ens|ENST00000273261NM_015541NM_015541Hs.51805526018LRIG1leucine-rich repeats and immunoglobulin-like domains 1ENST00000496559Homo sapiens leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1), mRNA [NM_015541]chr36642965666429597
A_22_P0001132514.7114.4513.8214.0514.6114.10DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-OST4-2:3|linc|lnc-OST4-2:2AK125769Hs.666730lnc-OST4-2lnc-OST4-2:3LNCipedia lincRNA (lnc-OST4-2), lincRNA [lnc-OST4-2:3]chr22723742827237369
A_22_P000008817.667.627.917.986.877.96DetectedDetectedDetectedDetectedDetectedDetectedref|NM_001010881|ens|ENST00000433342|linc|lnc-AGTRAP-1:1|ref|XM_006710068NM_001010881NM_001010881Hs.730573284498C1orf167chromosome 1 open reading frame 167ENST00000433342Homo sapiens chromosome 1 open reading frame 167 (C1orf167), mRNA [NM_001010881]chr11182610611826165
A_24_P14330110.9911.0810.8511.6011.5112.08DetectedDetectedDetectedDetectedDetectedDetectedref|NM_181337|ens|ENST00000274766|gb|AF181722NM_181337NM_181337Hs.697888353219KAAG1kidney associated antigen 1ENST00000274766Homo sapiens kidney associated antigen 1 (KAAG1), mRNA [NM_181337]chr62435760524357664
A_22_P000103339.289.059.439.448.579.20DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000452888|linc|lnc-MYB-5:1|linc|TCONS_00011377ENST00000452888chr6134957640134957699
A_23_P21540612.8013.1213.2112.6112.0212.57DetectedDetectedDetectedDetectedDetectedDetectedref|NM_018890|ref|NM_006908|ens|ENST00000348035|gb|AK054993NM_018890NM_018890Hs.4138125879RAC1ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)ENST00000348035Homo sapiens ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) (RAC1), transcript variant Rac1b, mRNA [NM_018890]chr764430136443072
A_22_P000115504.793.143.225.264.604.36Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedlinc|lnc-PCDH18-1:4|linc|lnc-PCDH18-1:1|linc|TCONS_00009123|linc|TCONS_00008582Hs.738310lnc-PCDH18-1lnc-PCDH18-1:4LNCipedia lincRNA (lnc-PCDH18-1), lincRNA [lnc-PCDH18-1:4]chr4138628424138628365
A_21_P000309611.2011.6511.2910.3710.7910.23DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-IL5RA-3:1|linc|TCONS_00006396lnc-IL5RA-3lnc-IL5RA-3:1LNCipedia lincRNA (lnc-IL5RA-3), lincRNA [lnc-IL5RA-3:1]chr321392722139213
A_21_P00137386.057.387.477.076.947.19DetectedDetectedDetectedDetectedDetectedDetectedlinc|TCONS_l2_00030040|gb|DQ673932|gb|DQ673931XLOC_l2_015315BROAD Institute lincRNA (XLOC_l2_015315), lincRNA [TCONS_l2_00030040]chr9102128039102127202
A_21_P00102866.186.626.547.027.337.43DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-PRDM15-1:1|linc|TCONS_00029147lnc-PRDM15-1lnc-PRDM15-1:1LNCipedia lincRNA (lnc-PRDM15-1), lincRNA [lnc-PRDM15-1:1]chr214320907743209018
A_24_P33611310.8410.9010.9110.6710.7910.66DetectedDetectedDetectedDetectedDetectedDetectedref|NM_012295|ref|NM_001199281|ref|NM_001201429|ens|ENST00000620406NM_012295NM_012295Hs.51747823523CABIN1calcineurin binding protein 1ENST00000620406Homo sapiens calcineurin binding protein 1 (CABIN1), transcript variant 2, mRNA [NM_012295]chr222457442224574481
A_33_P33739919.169.219.328.959.619.77DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000437095|linc|lnc-ECEL1-1:1|linc|TCONS_00003513|gb|CN283607Hs.574600ENST0000043709517000424984468 GRN_ES Homo sapiens cDNA 5', mRNA sequence [CN283607]chr2233285490233285431
A_33_P32666194.853.665.443.645.083.67Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedens|ENST00000547602|ref|XR_245977|ref|XR_247813|ref|XR_253055XR_245977XR_245977Hs.382689728114LOC728114uncharacterized LOC728114ENST00000547602PREDICTED: Homo sapiens uncharacterized LOC728114 (LOC728114), misc_RNA [XR_245977]chr124841364448413585
A_33_P33614127.917.507.437.867.417.83DetectedDetectedDetectedDetectedDetectedDetectedref|NM_018420|ens|ENST00000369502|ens|ENST00000369503|ref|XR_426622NM_018420NM_018420Hs.12548255356SLC22A15solute carrier family 22, member 15ENST00000369502Homo sapiens solute carrier family 22, member 15 (SLC22A15), mRNA [NM_018420]chr1116569583116569642
A_33_P33499277.367.117.037.297.447.25DetectedDetectedDetectedDetectedDetectedDetectedens|ENST00000467220|gb|CR627036|tc|NP1276298CR62703655112WDR60WD repeat domain 60ENST00000467220WD repeat domain 60 [Source:HGNC Symbol;Acc:HGNC:21862] [ENST00000467220]chr7158695283158695342
A_22_P000238803.193.953.133.183.163.13Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedlinc|lnc-ANKMY2-1:1|tc|THC2776638lnc-ANKMY2-1lnc-ANKMY2-1:1Q3V199_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]chr71673558416735525
A_22_P000025946.697.446.687.026.846.29DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-C19orf54-1:1lnc-C19orf54-1lnc-C19orf54-1:1LNCipedia lincRNA (lnc-C19orf54-1), lincRNA [lnc-C19orf54-1:1]chr194130226141302202
A_22_P000193573.193.123.143.193.813.27Not DetectedNot DetectedNot DetectedNot DetectedNot DetectedNot Detectedlinc|lnc-UMPS-1:1|gb|BF727361BF727361Hs.581599lnc-UMPS-1lnc-UMPS-1:1by20d10.y1 Human Lens cDNA (Un-normalized, unamplified): BY Homo sapiens cDNA clone by20d10 5', mRNA sequence [BF727361]chr3124506545124506604
A_22_P000090956.475.606.158.696.005.45Not DetectedDetectedDetectedDetectedDetectedDetectedlinc|lnc-LHX2-2:1lnc-LHX2-2lnc-LHX2-2:1LNCipedia lincRNA (lnc-LHX2-2), lincRNA [lnc-LHX2-2:1]chr9126514156126514215

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.


ProbeNameTreatment_1Treatment_2Treatment_3Control_1Control_2Control_3foldChangelog2FoldChangeregulationpvalsignificantPrimaryAccessionEntrezGeneIDGeneSymbolGeneNameDescriptionchrstartendGOKEGG
A_33_P324416519.4919.4919.4919.4919.4919.4910down0.00yesref|NR_003287|ref|NR_046235|gb|FB355642|gb|AK131444100008589RNA28S5RNA, 28S ribosomal 5Homo sapiens RNA, 28S ribosomal 5 (RNA28S5), ribosomal RNA [NR_003287]chrUn_gl000220117142117201
A_23_P13709710.4610.4610.688.1288.061.310.39up0.00yesref|NM_006517|ens|ENST00000587091|ref|XM_005262294|gb|U053156567SLC16A2solute carrier family 16, member 2 (thyroid hormone transporter)Homo sapiens solute carrier family 16, member 2 (thyroid hormone transporter) (SLC16A2), mRNA [NM_006517]chrX7375351473753573GO: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_P2045412.1912.1212.1911.1111.2011.101.090.13up0.00yesref|NM_001098398|ref|NM_004371|gb|CB2408271314COPAcoatomer protein complex, subunit alphaHomo sapiens coatomer protein complex, subunit alpha (COPA), transcript variant 1, mRNA [NM_001098398]chr1160258482160258423GO: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_P001432912.1812.2112.1711.1611.1011.271.090.12up0.00yesens|ENST00000563307|gb|BC053935|gb|AK090752|gb|AX7466001459CSNK2A2casein kinase 2, alpha prime polypeptidecasein kinase 2, alpha prime polypeptide [Source:HGNC Symbol;Acc:HGNC:2459] [ENST00000563307]chr165819355458193495GO: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_P0001485010.5010.7410.689.128.978.951.180.24up0.00yesens|ENST00000607654|ens|ENST00000416861|linc|lnc-SLC4A3-1:1|gb|AK056734Homo sapiens cDNA FLJ32172 fis, clone PLACE6000555. [AK056734]chr2220551715220551774
A_23_P35057411.7311.7111.7811.2611.2411.311.040.06up0.00yesref|NM_001002901|ref|NM_001288831|ref|NM_001288832|ref|NM_001288829127943FCRLBFc receptor-like BHomo sapiens Fc receptor-like B (FCRLB), transcript variant 1, mRNA [NM_001002901]chr1161697713161697772GO:0005737(cytoplasm);GO:0005783(endoplasmic reticulum);GO:0050777(negative regulation of immune response)
A_33_P329853911.5011.5311.4412.6512.4712.460.92-0.12down0.00yesref|NM_000039|ens|ENST00000236850|ens|ENST00000375323|ens|ENST00000375320335APOA1apolipoprotein A-IHomo sapiens apolipoprotein A-I (APOA1), mRNA [NM_000039]chr11116706700116706641GO: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_P7380110.7910.7610.8410.2610.2910.341.050.07up0.00yesref|NM_001006640|ref|NM_004780|ref|NM_001006639|ens|ENST000006193979338TCEAL1transcription elongation factor A (SII)-like 1Homo sapiens transcription elongation factor A (SII)-like 1 (TCEAL1), transcript variant 3, mRNA [NM_001006640]chrX102885333102885392GO: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_P15023812.9612.8712.9813.5913.6713.570.95-0.07down0.00yesref|NM_031450|ref|NM_001135635|ens|ENST00000449692|ens|ENST0000043857683638C11orf68chromosome 11 open reading frame 68Homo sapiens chromosome 11 open reading frame 68 (C11orf68), transcript variant 2, mRNA [NM_031450]chr116568456465684505
A_33_P337142512.8512.8512.8113.2413.1913.270.97-0.04down0.00yesref|NM_020451|ref|NM_206926|ens|ENST00000494537|ens|ENST0000035417757190SEPN1selenoprotein N, 1Homo sapiens selenoprotein N, 1 (SEPN1), transcript variant 1, mRNA [NM_020451]chr12614211726142176GO:0003674(molecular_function);GO:0005509(calcium ion binding);GO:0005515(protein binding);GO:0005789(endoplasmic reticulum membrane);GO:0008150(biological_process)
A_22_P0001317911.3211.1511.3812.5312.4512.380.91-0.14down0.00yeslinc|lnc-RNF144B-1:1|gb|AK098665|tc|THC2543869lnc-RNF144B-1lnc-RNF144B-1:1Homo sapiens cDNA FLJ25799 fis, clone TST07088. [AK098665]chr61853616118536220
A_19_P003258107.797.907.6298.948.950.87-0.21down0.00yesref|NR_027005|ens|ENST00000484801|gb|AK090984|tc|THC250297980759KHDC1KH homology domain containing 1Homo sapiens KH homology domain containing 1 (KHDC1), transcript variant 3, non-coding RNA [NR_027005]chr67398473673984677GO:0003723(RNA binding);GO:0016021(integral to membrane)
A_21_P00096357.727.817.858.408.358.410.93-0.11down0.00yeslinc|lnc-RTTN-2:1|linc|TCONS_00026726lnc-RTTN-2lnc-RTTN-2:1LNCipedia lincRNA (lnc-RTTN-2), lincRNA [lnc-RTTN-2:1]chr186800478168004574
A_22_P000159349.739.829.809.159.039.161.070.10up0.00yeslinc|lnc-TCP11L2-2:1|gb|BG199486|tc|THC2776961lnc-TCP11L2-2lnc-TCP11L2-2:1RST18770 Athersys RAGE Library Homo sapiens cDNA, mRNA sequence [BG199486]chr12106497094106497153
A_24_P6863113.5713.5013.5214.2614.3114.450.94-0.08down0.00yesref|NM_175065|ens|ENST00000331128|gb|BC172330|gb|BC132811317772HIST2H2ABhistone cluster 2, H2abHomo sapiens histone cluster 2, H2ab (HIST2H2AB), mRNA [NM_175065]chr1149859244149859185GO: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_P882787.727.527.636.806.826.741.120.17up0.00yesref|NM_020366|ens|ENST00000400017|ens|ENST00000553927|ens|ENST0000055532257096RPGRIP1retinitis pigmentosa GTPase regulator interacting protein 1Homo sapiens retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1), mRNA [NM_020366]chr142181330321816336GO: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_P380837112.0912.0412.0411.7111.7411.671.030.04up0.00yesgb|AL833480|gb|AK125186|tc|THC2502358|tc|THC2566333283911LOC283911uncharacterized LOC283911Homo sapiens mRNA; cDNA DKFZp686C2429 (from clone DKFZp686C2429). [AL833480]chr163438863834388697
A_33_P33824238.378.308.327.767.727.611.080.11up0.00yesref|NM_182498|ens|ENST00000300811|gb|BC045799|tc|THC2472513126299ZNF428zinc finger protein 428Homo sapiens zinc finger protein 428 (ZNF428), mRNA [NM_182498]chr194411145144111392GO:0046872(metal ion binding)
A_23_P6873012.4212.3712.5111.8511.7611.831.050.07up0.00yesref|NM_003681|ens|ENST00000291565|ens|ENST00000468090|ref|XM_0052611988566PDXKpyridoxal (pyridoxine, vitamin B6) kinaseHomo sapiens pyridoxal (pyridoxine, vitamin B6) kinase (PDXK), mRNA [NM_003681]chr214518180845181867GO: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_P321470512.7213.0512.4315.4015.3815.080.83-0.26down0.00yesref|NM_001100418|ref|NM_001100419|ens|ENST00000597371|ens|ENST0000059837555049C19orf60chromosome 19 open reading frame 60Homo sapiens chromosome 19 open reading frame 60 (C19orf60), transcript variant 1, mRNA [NM_001100418]chr191870168818702918GO:0005515(protein binding)
A_22_P0001484510.9411.1311.0610.3110.2210.191.080.11up0.00yeslinc|lnc-SLC4A10-2:1|tc|THC2638507lnc-SLC4A10-2lnc-SLC4A10-2:1S79876 dipeptidyl peptidase IV {Homo sapiens} (exp=-1; wgp=0; cg=0), partial (94%) [THC2638507]chr2162929769162929828
A_23_P3172511.9512.0712.0611.3111.4411.351.060.08up0.00yesref|NM_001715|ens|ENST00000526097|ens|ENST00000259089|ref|XM_005272390640BLKBLK proto-oncogene, Src family tyrosine kinaseHomo sapiens BLK proto-oncogene, Src family tyrosine kinase (BLK), mRNA [NM_001715]chr81142185811421917GO: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_P00146189.639.839.718.858.718.861.100.14up0.00yesref|XR_246615|ref|XR_249555|ref|XR_251536|linc|lnc-ATP5I-1:1101928521LOC101928521uncharacterized LOC101928521PREDICTED: Homo sapiens uncharacterized LOC101928521 (RP11-1191J2.2), ncRNA [XR_246615]chr4647379647320
A_23_P646118.438.818.916.656.896.751.290.37up0.00yesref|NM_176798|ref|NM_001277204|ref|NM_176796|ref|NM_0012772055031P2RY6pyrimidinergic receptor P2Y, G-protein coupled, 6Homo sapiens pyrimidinergic receptor P2Y, G-protein coupled, 6 (P2RY6), transcript variant 2, mRNA [NM_176798]chr117300862573008684GO: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_P0000606011.9511.6511.6813.2013.2013.010.90-0.16down0.00yeslinc|lnc-FAM131B-1:2|gb|AB074268|gb|CU690101|tc|THC2631669lnc-FAM131B-1lnc-FAM131B-1:2Homo sapiens primary neuroblastoma cDNA, clone:Nbla10687, full insert sequence. [AB074268]chr7142983199142983140
A_33_P33268728.588.698.677.867.948.031.090.12up0.00yeschr132341111123411052
A_23_P35184410.4910.0910.0711.9111.9111.780.86-0.22down0.00yesref|NM_001764|ens|ENST00000368168|ens|ENST00000451207|gb|M28826910CD1BCD1b moleculeHomo sapiens CD1b molecule (CD1B), mRNA [NM_001764]chr1158297780158297740GO: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_P21245813.7813.7613.6913.4013.3813.341.030.04up0.00yesref|NM_013336|ens|ENST00000424880|ens|ENST00000243253|ens|ENST0000048395629927SEC61A1Sec61 alpha 1 subunit (S. cerevisiae)Homo sapiens Sec61 alpha 1 subunit (S. cerevisiae) (SEC61A1), mRNA [NM_013336]chr3127789960127790019GO: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_P21362411.7712.1012.1510.4110.4110.611.150.20up0.00yesref|NM_001130841|ref|NM_003729|ens|ENST00000370128|ref|XM_0052712988634RTCARNA 3'-terminal phosphate cyclaseHomo sapiens RNA 3'-terminal phosphate cyclase (RTCA), transcript variant 1, mRNA [NM_001130841]chr1100758204100758263GO: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_P39211013.4213.2113.6411.2911.7011.341.170.23up0.00yesref|NM_182707|ref|NM_001130167|ref|NM_001130168|ref|NM_021016440533PSG8pregnancy specific beta-1-glycoprotein 8Homo sapiens pregnancy specific beta-1-glycoprotein 8 (PSG8), transcript variant 1, mRNA [NM_182707]chr194325854943258490GO:0005576(extracellular region)
A_22_P0001245615.2115.2215.1715.6015.6115.720.97-0.04down0.00yesref|NR_027687|ref|NR_027686|ens|ENST00000431158|ens|ENST00000444463284739LINC00176long intergenic non-protein coding RNA 176Homo sapiens long intergenic non-protein coding RNA 176 (LINC00176), transcript variant 2, long non-coding RNA [NR_027687]chr206266949662669555
A_23_P10396812.4712.2512.2113.1713.1913.250.93-0.10down0.00yesref|NM_012067|ens|ENST00000361640|gb|AF040639|gb|EU17623522977AKR7A3aldo-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]chr11961123319610614GO: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_P35772612.6112.5512.9610.2910.8510.491.210.27up0.00yesref|NM_182707|ref|NM_001130167|ref|NM_001130168|ref|NM_002782440533PSG8pregnancy specific beta-1-glycoprotein 8Homo sapiens pregnancy specific beta-1-glycoprotein 8 (PSG8), transcript variant 1, mRNA [NM_182707]chr194325920643259147GO:0005576(extracellular region)
A_33_P33309729.599.909.738.818.798.731.110.15up0.00yeschr4624773624714
A_23_P1244279.419.449.5610.6311.0610.930.87-0.20down0.00yesref|NM_012224|ref|NM_001199397|ref|NM_001199398|ref|NM_0011994004750NEK1NIMA-related kinase 1Homo sapiens NIMA-related kinase 1 (NEK1), transcript variant 2, mRNA [NM_012224]chr4170315411170315352GO: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_P00102407.377.437.598.228.178.140.91-0.13down0.00yesref|XR_425268|ref|XR_430370|ref|XR_433641|linc|lnc-CHAF1B-1:1102724630LOC102724630uncharacterized LOC102724630PREDICTED: Homo sapiens uncharacterized LOC102724630 (LOC102724630), ncRNA [XR_425268]chr213775713837757197
A_32_P8676314.4714.5414.3413.6613.7813.771.050.07up0.00yesref|NM_004613|ens|ENST00000469269|gb|AK126508|gb|AK0580317052TGM2transglutaminase 2Homo sapiens transglutaminase 2 (TGM2), transcript variant 1, mRNA [NM_004613]chr203675791236757853GO: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_P008117068.108.518.186.826.486.621.240.32up0.00yesref|NM_005578|ref|NM_001167671|ref|NM_001167672|ens|ENST000006163044026LPPLIM domain containing preferred translocation partner in lipomaHomo sapiens LIM domain containing preferred translocation partner in lipoma (LPP), transcript variant 1, mRNA [NM_005578]chr3188601619188601678GO: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_P1353366.826.826.757.467.557.340.91-0.13down0.00yesref|NR_002556|ref|NR_002557|ref|XM_006726617|tc|THC2546736388242LOC388242coiled-coil domain containing 101 pseudogeneHomo sapiens coiled-coil domain containing 101 pseudogene (LOC388242), non-coding RNA [NR_002556]chr162947635329476294
A_22_P000164778.038.298.167.417.337.311.110.15up0.00yeslinc|lnc-TMEM86A-1:1|tc|THC2607151lnc-TMEM86A-1lnc-TMEM86A-1:1HSU27831 striatum-enriched phosphatase {Homo sapiens} (exp=-1; wgp=0; cg=0), partial (5%) [THC2607151]chr111876202518762084
A_19_P008127017.047.206.758.488.808.570.81-0.30down0.00yeschr650417265041785
A_33_P331782512.8712.6812.8613.4213.4313.480.95-0.07down0.00yesref|NM_002524|ens|ENST00000369535|gb|AF493919|gb|BT0197344893NRASneuroblastoma RAS viral (v-ras) oncogene homologHomo sapiens neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), mRNA [NM_002524]chr1115251224115251165GO: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_P340793710.7410.6810.8611.2811.3211.290.95-0.07down0.00yesref|NM_018390|ref|NR_028057|ens|ENST00000381663|ens|ENST0000039901255344PLCXD1phosphatidylinositol-specific phospholipase C, X domain containing 1Homo sapiens phosphatidylinositol-specific phospholipase C, X domain containing 1 (PLCXD1), transcript variant 1, mRNA [NM_018390]chrX208260208319GO:0006629(lipid metabolic process);GO:0008081(phosphoric diester hydrolase activity)
A_24_P39806412.4512.5612.6012.0912.0512.021.040.06up0.00yesens|ENST00000378078|gb|D87447|tc|THC25149209827RGP1RGP1 retrograde golgi transport homolog (S. cerevisiae)RGP1 retrograde golgi transport homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:21965] [ENST00000378078]chr93575765635757715GO: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_P1825013.6013.6013.6713.131313.161.040.06up0.00yesref|NR_003663|ens|ENST00000443452|ens|ENST00000331369|gb|BC040550388965FUNDC2P2FUN14 domain containing 2 pseudogene 2Homo sapiens FUN14 domain containing 2 pseudogene 2 (FUNDC2P2), non-coding RNA [NR_003663]chr28451828484518343
A_33_P341543013.1013.0813.2613.7813.8113.710.95-0.07down0.00yesref|NM_005346|ens|ENST00000545241|ens|ENST00000391548|ens|ENST000003756503304HSPA1Bheat shock 70kDa protein 1BHomo sapiens heat shock 70kDa protein 1B (HSPA1B), mRNA [NM_005346]chr63179787031797929GO: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_P000153798.928.868.689.849.829.630.90-0.15down0.00yesref|XR_424822|ref|XR_429964|ref|XR_430800|ref|XR_433386101929494LOC101929494uncharacterized LOC101929494PREDICTED: Homo sapiens uncharacterized LOC101929494 (LOC101929494), transcript variant X3, ncRNA [XR_424822]chr173660763736607578
A_23_P5622810.6811.0210.8811.9211.7911.850.92-0.13down0.00yesref|NM_016573|ref|NM_001288999|ref|NM_001288998|ens|ENST0000020355651291GMIPGEM interacting proteinHomo sapiens GEM interacting protein (GMIP), transcript variant 1, mRNA [NM_016573]chr191974053519740476GO: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_P00082339.789.629.7010.3410.2110.350.94-0.09down0.00yeslinc|lnc-PABPC3-1:2|linc|lnc-PABPC3-1:1|linc|TCONS_00022147|linc|TCONS_00021734lnc-PABPC3-1lnc-PABPC3-1:2LNCipedia lincRNA (lnc-PABPC3-1), lincRNA [lnc-PABPC3-1:2]chr132569299125693050
A_23_P3607548.188.638.565.856.315.481.440.52up0.00yesref|NM_005099|gb|AB014588|gb|BC063293|gb|AY3588869507ADAMTS4ADAM metallopeptidase with thrombospondin type 1 motif, 4Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif, 4 (ADAMTS4), mRNA [NM_005099]chr1161159705161159646GO: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_P33367609.919.509.808.278.478.511.160.21up0.00yesref|NM_018849|ref|NM_000443|ref|NM_018850|ens|ENST000002657235244ABCB4ATP-binding cassette, sub-family B (MDR/TAP), member 4Homo sapiens ATP-binding cassette, sub-family B (MDR/TAP), member 4 (ABCB4), transcript variant B, mRNA [NM_018849]chr78703144287031383GO: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_P2501367.486.837.524.333.943.311.890.91up0.00yesref|NM_175768|ref|NM_001166247|ref|NM_021956|ens|ENST000003691382898GRIK2glutamate receptor, ionotropic, kainate 2Homo sapiens glutamate receptor, ionotropic, kainate 2 (GRIK2), transcript variant 2, mRNA [NM_175768]chr6102516621102516680GO: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_P000141497.447.107.019.128.669.020.80-0.31down0.00yesens|ENST00000577329|linc|lnc-SCN4A-1:1chr176205054562050486
A_33_P34180259.339.249.627.798.088.121.180.23up0.00yesref|NM_001334|ens|ENST00000433477|ens|ENST00000573499|gb|BC0492061519CTSOcathepsin OHomo sapiens cathepsin O (CTSO), mRNA [NM_001334]chr4156845446156845387GO:0004197(cysteine-type endopeptidase activity);GO:0005764(lysosome);GO:0006508(proteolysis)04142(Lysosome)
A_33_P37647449.659.049.2111.3711.1811.010.83-0.27down0.00yestc|THC2596880HSU02032 ribosomal protein L23a {Homo sapiens} (exp=-1; wgp=0; cg=0), partial (70%) [THC2596880]chr175914823559148294GO:0003723(RNA binding);GO:0003735(structural constituent of ribosome);GO:0005622(intracellular);GO:0006412(translation)
A_21_P000497710.5310.4910.5811.0710.9611.140.95-0.07down0.00yeslinc|lnc-FAM120B-6:2|linc|TCONS_00012028lnc-FAM120B-6lnc-FAM120B-6:2LNCipedia lincRNA (lnc-FAM120B-6), lincRNA [lnc-FAM120B-6:2]chr6170455160170455219
A_23_P6512910.9910.6510.7811.8411.7011.750.92-0.12down0.00yesref|NM_032840|ens|ENST00000301463|gb|BC136312|gb|AK02770684926SPRYD3SPRY domain containing 3Homo sapiens SPRY domain containing 3 (SPRYD3), mRNA [NM_032840]chr125345870553458646
A_24_P30964512.5212.4612.5111.4411.7811.591.080.11up0.00yesref|NM_017901|ref|NM_001143819|ref|NM_001301214|ens|ENST0000055112753373TPCN1two pore segment channel 1Homo sapiens two pore segment channel 1 (TPCN1), transcript variant 2, mRNA [NM_017901]chr12113730870113731124GO: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_P000050675.805.505.684.674.464.331.260.34up0.00yesens|ENST00000545293|ens|ENST00000543611|linc|lnc-DENR-2:2|linc|lnc-DENR-2:1chr12123200160123200219
A_23_P16911211.7711.5111.5212.4712.5812.720.92-0.12down0.00yesref|NM_013291|ens|ENST00000526271|ens|ENST00000620219|ens|ENST0000061614029894CPSF1cleavage and polyadenylation specific factor 1, 160kDaHomo sapiens cleavage and polyadenylation specific factor 1, 160kDa (CPSF1), mRNA [NM_013291]chr8145619722145619663GO: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_P460397.666.728.103.883.323.222.161.11up0.00yesref|NM_032738|ref|NM_001184866|ref|NM_001184867|ref|NM_00118487084824FCRLAFc receptor-like AHomo sapiens Fc receptor-like A (FCRLA), transcript variant 2, mRNA [NM_032738]chr1161683792161683851GO:0005576(extracellular region);GO:0005737(cytoplasm);GO:0030154(cell differentiation)
A_22_P0000753112.1512.0912.1511.7811.6311.661.040.05up0.00yesref|NR_029373|ref|NR_029374|linc|lnc-HADH-1:3|linc|lnc-HADH-1:1641518LEF1-AS1LEF1 antisense RNA 1Homo sapiens LEF1 antisense RNA 1 (LEF1-AS1), transcript variant 1, long non-coding RNA [NR_029373]chr4109097484109097543
A_33_P334144210.3310.109.9811.3211.2311.090.90-0.15down0.00yesref|NM_000395|ens|ENST00000262825|ens|ENST00000403662|ref|XM_0052613401439CSF2RBcolony 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]chr223733438837334447GO: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_P26508810.0410.0810.279.449.269.271.090.12up0.00yesens|ENST00000393758|ens|ENST00000544474|ens|ENST00000164640|gb|AK12701657595PDZD4PDZ domain containing 4PDZ domain containing 4 [Source:HGNC Symbol;Acc:HGNC:21167] [ENST00000393758]chrX153068362153068303GO:0005938(cell cortex)
A_33_P337455910.9311.1410.8912.2112.1812.590.89-0.17down0.00yesref|NR_024448|ens|ENST00000444220|ens|ENST00000437294|ens|ENST0000043586891316GUSBP11glucuronidase, beta pseudogene 11Homo sapiens glucuronidase, beta pseudogene 11 (GUSBP11), non-coding RNA [NR_024448]chr222405725824057199
A_33_P33167287.267.317.317.647.657.770.95-0.08down0.00yesens|ENST00000567850|ens|ENST00000564895DNM1 pseudogene 34 [Source:HGNC Symbol;Acc:HGNC:35181] [ENST00000567850]chr157559493575594876
A_24_P33366312.5412.5112.8511.4611.1211.391.120.16up0.00yesref|NM_002748|ens|ENST00000518703|ens|ENST00000403865|ref|XM_0052545365597MAPK6mitogen-activated protein kinase 6Homo sapiens mitogen-activated protein kinase 6 (MAPK6), mRNA [NM_002748]chr155235690752356966GO: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_P0001890211.2111.4611.3510.3610.5710.541.080.11up0.00yeslinc|lnc-C11orf39-3:1|gb|DA375949lnc-C11orf39-3lnc-C11orf39-3:1DA375949 BRTHA2 Homo sapiens cDNA clone BRTHA2007423 5', mRNA sequence [DA375949]chr11131747657131747598
A_21_P000849010.9711.8210.7614.5714.5514.030.78-0.36down0.00yeslinc|lnc-RTL1-6:1|linc|TCONS_00022880lnc-RTL1-6lnc-RTL1-6:1LNCipedia lincRNA (lnc-RTL1-6), lincRNA [lnc-RTL1-6:1]chr14101820284101820225
A_33_P322637711.7211.8911.7611.3511.2811.301.040.06up0.00yesref|NM_005042|ref|NM_001110213|ens|ENST00000381847|ens|ENST000005756575555PRH2proline-rich protein HaeIII subfamily 2Homo sapiens proline-rich protein HaeIII subfamily 2 (PRH2), transcript variant 1, mRNA [NM_005042]chr121108362411083683GO:0005515(protein binding);GO:0005615(extracellular space)04970(Salivary secretion)
A_33_P32575687.076.976.727.877.957.820.88-0.19down0.00yesens|ENST00000373851|gb|AK097636|tc|THC272128411064CNTRLcentriolincentriolin [Source:HGNC Symbol;Acc:HGNC:1858] [ENST00000373851]chr9123912863123912922GO: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_P0001102010.8110.8010.7111.5111.5411.310.94-0.09down0.00yeslinc|lnc-NT5C-2:1lnc-NT5C-2lnc-NT5C-2:1LNCipedia lincRNA (lnc-NT5C-2), lincRNA [lnc-NT5C-2:1]chr177314141673141357
A_33_P334640317.5917.5917.4817.8917.9217.970.98-0.03down0.00yesref|NM_001099285|ref|NM_002823|ens|ENST00000397729|ens|ENST000003930735757PTMAprothymosin, alphaHomo sapiens prothymosin, alpha (PTMA), transcript variant 1, mRNA [NM_001099285]chr2232577214232577560GO: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_P32666468.388.508.529.079.019.210.93-0.10down0.00yesref|NM_138813|ref|NM_001178002|ref|NR_047593|ens|ENST00000533107148229ATP8B3ATPase, aminophospholipid transporter, class I, type 8B, member 3Homo sapiens ATPase, aminophospholipid transporter, class I, type 8B, member 3 (ATP8B3), transcript variant 1, mRNA [NM_138813]chr1918000031797004GO: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_P10468911.7711.6711.6511.2111.3211.291.040.05up0.00yesref|NM_021975|ref|NM_001145138|ref|NM_001243984|ref|NM_0012439855970RELAv-rel avian reticuloendotheliosis viral oncogene homolog AHomo sapiens v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), transcript variant 1, mRNA [NM_021975]chr116542171065421651GO: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_P16089614.1214.5514.3611.3212.0510.981.250.33up0.00yesref|NM_177478|ens|ENST00000321339|gb|HQ258558|gb|BC03441994033FTMTferritin mitochondrialHomo sapiens ferritin mitochondrial (FTMT), mRNA [NM_177478]chr5121188259121188318GO: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_P000117711.7111.5612.279.799.599.231.240.31up0.00yeslinc|lnc-FAM72C-2:1|ref|XM_006711090|ref|XM_006726339|linc|TCONS_00000639lnc-FAM72C-2lnc-FAM72C-2:1PREDICTED: Homo sapiens myomegalin-like (LOC100996723), mRNA [XM_006711090]chr1144506631144506690
A_33_P325771410.6510.7210.929.8310.019.971.080.12up0.00yesref|NM_001025|ens|ENST00000296674|gb|M32219|gb|BX6475636228RPS23ribosomal protein S23Homo sapiens ribosomal protein S23 (RPS23), mRNA [NM_001025]chr58156934981569290GO: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_P339439510.8211.0911.269.809.629.901.130.18up0.00yesref|NM_001270384|ref|NM_198549|ens|ENST00000370791|ens|ENST00000443751374986FAM73Afamily with sequence similarity 73, member AHomo sapiens family with sequence similarity 73, member A (FAM73A), transcript variant 2, mRNA [NM_001270384]chr17834375478343813GO:0016021(integral to membrane)
A_22_P000125577.737.987.927.147.177.251.100.13up0.00yesref|NR_033374|linc|lnc-PTGES2-1:4|linc|lnc-PTGES2-1:1|linc|lnc-PTGES2-1:5100289019SLC25A25-AS1SLC25A25 antisense RNA 1Homo sapiens SLC25A25 antisense RNA 1 (SLC25A25-AS1), long non-coding RNA [NR_033374]chr9130876872130876813
A_19_P0032289812.2312.2312.2111.9811.9911.891.020.03up0.00yesref|NR_026551|ens|ENST00000448692|ens|ENST00000380333|tc|THC2501410340591CA5BP1carbonic anhydrase VB pseudogene 1Homo sapiens carbonic anhydrase VB pseudogene 1 (CA5BP1), non-coding RNA [NR_026551]chrX1569384215693901GO:0004089(carbonate dehydratase activity);GO:0005739(mitochondrion);GO:0008152(metabolic process);GO:0008270(zinc ion binding)
A_23_P5786811.5011.3111.2512.2812.5712.670.91-0.14down0.00yesref|NM_000666|ref|NM_001198895|ref|NM_001198898|ref|NM_00119889795ACY1aminoacylase 1Homo sapiens aminoacylase 1 (ACY1), transcript variant 1, mRNA [NM_000666]chr35202297952023038GO: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_P14949412.3711.9812.4611.0210.8911.051.120.16up0.00yesref|NM_015600|ref|NM_001042472|ens|ENST00000481556|ens|ENST0000037654226090ABHD12abhydrolase domain containing 12Homo sapiens abhydrolase domain containing 12 (ABHD12), transcript variant 2, mRNA [NM_015600]chr202528866525288606GO: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_P21212910.9410.9411.0211.4511.6411.680.95-0.08down0.00yesref|NM_006974|ref|NM_001278170|ref|NM_001278173|ref|NM_0012781787581ZNF33Azinc finger protein 33AHomo sapiens zinc finger protein 33A (ZNF33A), transcript variant 2, mRNA [NM_006974]chr103830622138306280GO: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_P22179911.4111.4611.051312.5812.980.88-0.18down0.00yesref|NM_003514|gb|BC071668|gb|BC032686|gb|BC0327568336HIST1H2AMhistone cluster 1, H2amHomo sapiens histone cluster 1, H2am (HIST1H2AM), mRNA [NM_003514]chr62786056627860507GO: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_P335303010.9810.8811.1110.3010.0410.101.080.12up0.00yesref|NM_003353|ens|ENST00000296099|tc|THC24767577349UCNurocortinHomo sapiens urocortin (UCN), mRNA [NM_003353]chr22753032427530265GO: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_P0000271410.7110.2710.3512.1511.8711.740.88-0.19down0.00yesens|ENST00000437035|ens|ENST00000421257|linc|lnc-C20orf197-3:9|linc|lnc-C20orf197-3:10MIR646 host gene (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:27659] [ENST00000437035]chr205888838658888445
A_33_P33925379.339.309.656.847.087.681.310.39up0.00yesref|NM_004614|ref|NM_001172645|ref|NM_001172644|ref|NM_0011726437084TK2thymidine kinase 2, mitochondrialHomo sapiens thymidine kinase 2, mitochondrial (TK2), transcript variant 1, mRNA [NM_004614]chr166654341166543352GO: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_P0000428211.0210.6510.3912.1612.1712.290.88-0.19down0.00yesref|NR_104131|ens|ENST00000456551|ens|ENST00000452922|linc|lnc-CNN3-3:8101928079LINC01057long intergenic non-protein coding RNA 1057Homo sapiens long intergenic non-protein coding RNA 1057 (LINC01057), long non-coding RNA [NR_104131]chr19512354095123481
A_23_P3701621110.7410.649.839.929.931.090.13up0.00yesref|NM_182969|ref|NM_001270381|ref|NM_001270380|ens|ENST00000531849143570XRRA1X-ray radiation resistance associated 1Homo sapiens X-ray radiation resistance associated 1 (XRRA1), transcript variant 1, mRNA [NM_182969]chr117455265074552591GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0010165(response to X-ray)
A_23_P506979.859.5210.128.028.398.121.200.27up0.00yesref|NM_006905|ref|NM_001297773|ref|NM_001184826|ref|NM_0011848255669PSG1pregnancy specific beta-1-glycoprotein 1Homo sapiens pregnancy specific beta-1-glycoprotein 1 (PSG1), transcript variant 1, mRNA [NM_006905]chr194337236543372306GO:0005576(extracellular region);GO:0007565(female pregnancy)
A_21_P00042366.206.446.095.155.375.291.180.24up0.00yeslinc|lnc-C5orf17-1:2|linc|lnc-C5orf17-1:1|linc|TCONS_00009905|linc|TCONS_00009904lnc-C5orf17-1lnc-C5orf17-1:2LNCipedia lincRNA (lnc-C5orf17-1), lincRNA [lnc-C5orf17-1:2]chr52432115524321214
A_33_P336348510.099.9910.1910.5410.5810.560.96-0.07down0.00yesref|NM_018013|ens|ENST00000477448|ens|ENST00000618129|ens|ENST0000031735755084SOBPsine oculis binding protein homolog (Drosophila)Homo sapiens sine oculis binding protein homolog (Drosophila) (SOBP), mRNA [NM_018013]chr6107827569107827628GO: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_P00008125.925.875.726.366.506.400.91-0.14down0.00yesref|NR_038458|linc|lnc-WFIKKN2-1:1|gb|AK123714|tc|THC2511559400604TOB1-AS1TOB1 antisense RNA 1Homo sapiens TOB1 antisense RNA 1 (TOB1-AS1), long non-coding RNA [NR_038458]chr174894560948945668
A_23_P13950012.8112.5612.901111.4110.771.150.21up0.00yesref|NM_030762|ens|ENST00000242728|gb|AY665467|gb|BC02596879365BHLHE41basic helix-loop-helix family, member e41Homo sapiens basic helix-loop-helix family, member e41 (BHLHE41), mRNA [NM_030762]chr122627369126273632GO: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_P000123545.205.385.426.276.206.550.84-0.25down0.00yeslinc|lnc-PRDX6-1:1lnc-PRDX6-1lnc-PRDX6-1:1LNCipedia lincRNA (lnc-PRDX6-1), lincRNA [lnc-PRDX6-1:1]chr1173572308173572367
A_33_P34222339.249.148.859.9910.1110.040.90-0.15down0.00yesref|NM_020894|ens|ENST00000389851|ens|ENST00000503548|gb|AB04096357654UVSSAUV-stimulated scaffold protein AHomo sapiens UV-stimulated scaffold protein A (UVSSA), mRNA [NM_020894]chr413816731381732GO: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_P000550310.2410.1810.149.619.369.311.080.11up0.00yeslinc|lnc-SBDS-2:2|linc|TCONS_00013856lnc-SBDS-2lnc-SBDS-2:2LNCipedia lincRNA (lnc-SBDS-2), lincRNA [lnc-SBDS-2:2]chr76679849866798439
A_23_P409568.558.428.707.897.867.741.090.13up0.00yesref|NM_016362|ref|NM_001134941|ref|NM_001302821|ref|NM_00130282251738GHRLghrelin/obestatin prepropeptideHomo sapiens ghrelin/obestatin prepropeptide (GHRL), transcript variant 1, mRNA [NM_016362]chr31032755210327493GO: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_IDGO_TermGO_functionGO_classS gene numberTS gene numberB gene numberTB gene numberpvalue
GO:0000786nucleosomecellular_component1233177892159223.95e-10
GO:0006271DNA strand elongation involved in DNA replicationbiological_process1113177833159222.66e-05
GO:0006334nucleosome assemblybiological_process12271778107159223.42e-05
GO:0006298mismatch repairbiological_process1012177833159220.00
GO:0000083regulation of transcription involved in G1/S phase of mitotic cell cyclebiological_process1310177825159220.00
GO:0032201telomere maintenance via semi-conservative replicationbiological_process1110177825159220.00
GO:0006284base-excision repairbiological_process1014177845159220.00
GO:0000723telomere maintenancebiological_process920177880159220.00
GO:0006281DNA repairbiological_process9551778317159220.00
GO:0070182DNA polymerase bindingmolecular_function6517788159220.00
GO:0000722telomere maintenance via recombinationbiological_process1010177829159220.00
GO:0007067mitosisbiological_process7471778268159220.00
GO:0000278mitotic cell cyclebiological_process6751778476159220.00
GO:0006260DNA replicationbiological_process9291778145159220.00
GO:0051461positive regulation of corticotropin secretionbiological_process12317783159220.00
GO:0032211negative regulation of telomere maintenance via telomerasebiological_process13517789159220.00
GO:0006270DNA-dependent DNA replication initiationbiological_process119177827159220.00
GO:0007044cell-substrate junction assemblybiological_process7417786159220.00
GO:0006285base-excision repair, AP site formationbiological_process95177810159220.00
GO:0022617extracellular matrix disassemblybiological_process6241778119159220.00
GO:0051923sulfationbiological_process6417787159220.00
GO:0000777condensed chromosome kinetochorecellular_component1018177883159220.00
GO:00515394 iron, 4 sulfur cluster bindingmolecular_function611177841159220.00
GO:0006289nucleotide-excision repairbiological_process1018177884159220.00
GO:0003697single-stranded DNA bindingmolecular_function819177891159220.01
GO:0021784postganglionic parasympathetic nervous system developmentbiological_process9317784159220.01
GO:2000643positive regulation of early endosome to late endosome transportbiological_process5317784159220.01
GO:0031262Ndc80 complexcellular_component10317784159220.01
GO:0045007depurinationbiological_process10317784159220.01
GO:0005658alpha DNA polymerase:primase complexcellular_component13317784159220.01
GO:0021615glossopharyngeal nerve morphogenesisbiological_process11317784159220.01
GO:0032369negative regulation of lipid transportbiological_process7317784159220.01
GO:0048010vascular endothelial growth factor receptor signaling pathwaybiological_process10221778112159220.01
GO:0051301cell divisionbiological_process5551778352159220.01
GO:0046982protein heterodimerization activitymolecular_function6631778415159220.01
GO:0017154semaphorin receptor activitymolecular_function65177812159220.01
GO:0071354cellular response to interleukin-6biological_process8417788159220.01
GO:0031681G-protein beta-subunit bindingmolecular_function5417788159220.01
GO:0031100organ regenerationbiological_process811177844159220.01
GO:0032793positive regulation of CREB transcription factor activitybiological_process146177817159220.01
GO:0048009insulin-like growth factor receptor signaling pathwaybiological_process106177817159220.01
GO:0006297nucleotide-excision repair, DNA gap fillingbiological_process117177822159220.01
GO:0005657replication forkcellular_component117177822159220.01
GO:2000352negative regulation of endothelial cell apoptotic processbiological_process117177822159220.01
GO:0005814centriolecellular_component1019177896159220.01
GO:0006325chromatin organizationbiological_process6421778261159220.01
GO:0009165nucleotide biosynthetic processbiological_process95177813159220.01
GO:0033235positive regulation of protein sumoylationbiological_process125177813159220.01
GO:0006283transcription-coupled nucleotide-excision repairbiological_process1113177858159220.01
GO:0000070mitotic sister chromatid segregationbiological_process87177823159220.01
GO:0006273lagging strand elongationbiological_process12317785159220.01
GO:0042799histone methyltransferase activity (H4-K20 specific)molecular_function11317785159220.01
GO:0030911TPR domain bindingmolecular_function6317785159220.01
GO:0018230peptidyl-L-cysteine S-palmitoylationbiological_process10317785159220.01
GO:0009157deoxyribonucleoside monophosphate biosynthetic processbiological_process10317785159220.01
GO:0051414response to cortisol stimulusbiological_process9317785159220.01
GO:0072015glomerular visceral epithelial cell developmentbiological_process11317785159220.01
GO:0038033positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathwaybiological_process7317785159220.01
GO:0008484sulfuric ester hydrolase activitymolecular_function6317785159220.01
GO:0050702interleukin-1 beta secretionbiological_process9317785159220.01
GO:0071897DNA biosynthetic processbiological_process88177829159220.01
GO:0002116semaphorin receptor complexcellular_component6417789159220.01
GO:0051147regulation of muscle cell differentiationbiological_process8217782159220.01
GO:0006272leading strand elongationbiological_process12217782159220.01
GO:0004832valine-tRNA ligase activitymolecular_function8217782159220.01
GO:0000727double-strand break repair via break-induced replicationbiological_process12217782159220.01
GO:0072144glomerular mesangial cell developmentbiological_process10217782159220.01
GO:0008476protein-tyrosine sulfotransferase activitymolecular_function7217782159220.01
GO:0031508centromeric heterochromatin assemblybiological_process13217782159220.01
GO:0002086diaphragm contractionbiological_process11217782159220.01
GO:0006478peptidyl-tyrosine sulfationbiological_process8217782159220.01
GO:0034683alphav-beta3 integrin complexcellular_component9217782159220.01
GO:0006438valyl-tRNA aminoacylationbiological_process13217782159220.01
GO:0050748negative regulation of lipoprotein metabolic processbiological_process7217782159220.01
GO:2000766negative regulation of cytoplasmic translationbiological_process10217782159220.01
GO:0042351'de novo' GDP-L-fucose biosynthetic processbiological_process12217782159220.01
GO:0090188negative regulation of pancreatic juice secretionbiological_process9217782159220.01
GO:0032226positive regulation of synaptic transmission, dopaminergicbiological_process11217782159220.01
GO:0021793chemorepulsion of branchiomotor axonbiological_process10217782159220.01
GO:0050923regulation of negative chemotaxisbiological_process6217782159220.01
GO:0046104thymidine metabolic processbiological_process11217782159220.01
GO:0032202telomere assemblybiological_process7217782159220.01
GO:0004797thymidine kinase activitymolecular_function10217782159220.01
GO:0006206pyrimidine base metabolic processbiological_process97177824159220.01
GO:0000790nuclear chromatincellular_component13261778149159220.01
GO:0005178integrin bindingmolecular_function6201778107159220.01
GO:0001974blood vessel remodelingbiological_process69177836159220.02
GO:0010811positive regulation of cell-substrate adhesionbiological_process610177842159220.02
GO:0007160cell-matrix adhesionbiological_process618177894159220.02
GO:0000086G2/M transition of mitotic cell cyclebiological_process8281778165159220.02
GO:0014065phosphatidylinositol 3-kinase cascadebiological_process107177825159220.02
GO:1900034regulation of cellular response to heatbiological_process79177837159220.02
GO:0045806negative regulation of endocytosisbiological_process74177810159220.02
GO:0001921positive regulation of receptor recyclingbiological_process94177810159220.02
GO:0045792negative regulation of cell sizebiological_process74177810159220.02
GO:0006081cellular aldehyde metabolic processbiological_process54177810159220.02
GO:0016572histone phosphorylationbiological_process94177810159220.02
GO:0030166proteoglycan biosynthetic processbiological_process84177810159220.02
GO:0034260negative regulation of GTPase activitybiological_process154177810159220.02

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_idpathway_nameS gene numberTS gene numberB gene numberTB gene numberpvalue
ko05322Systemic lupus erythematosus137133059491.60e-05
ko03410Base excision repair97132659490.00
ko05203Viral carcinogenesis147135759490.01
ko05204Chemical carcinogenesis2713259490.01
ko03030DNA replication77132559490.02
ko04151PI3K-Akt signaling pathway1971310259490.03
ko00052Galactose metabolism|04973:Carbohydrate digestion and absorption47131359490.06
ko00500Starch and sucrose metabolism47131359490.06
ko00980Metabolism of xenobiotics by cytochrome P4503713859490.06
ko01212Fatty acid metabolism|01040:Biosynthesis of unsaturated fatty acids107135059490.07
ko00240Pyrimidine metabolism77133159490.07
ko04142Lysosome137137059490.07
ko00480Glutathione metabolism67132859490.11
ko04071Sphingolipid signaling pathway47131659490.12
ko01220Degradation of aromatic compounds|00010:Glycolysis / Gluconeogenesis|00040:Pentose and glucuronate interconversions|00561:Glycerolipid metabolism1713159490.12
ko00010Glycolysis / Gluconeogenesis|00620:Pyruvate metabolism|00640:Propanoate metabolism|00270:Cysteine and methionine metabolism|04922:Glucagon signaling pathway67132959490.13
ko04921Oxytocin signaling pathway37131159490.14
ko00531Glycosaminoglycan degradation47131759490.14
ko00760Nicotinate and nicotinamide metabolism47131759490.14
ko04114Oocyte meiosis47131759490.14
ko04974Protein digestion and absorption67133059490.14
ko00512Mucin type O-glycan biosynthesis57132459490.15
ko04510Focal adhesion2713659490.16
ko04122Sulfur relay system2713659490.16
ko04140Regulation of autophagy47131859490.16
ko00532Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate47131859490.16
ko00310Lysine degradation87134559490.16
ko00562Inositol phosphate metabolism117136759490.17
ko00600Sphingolipid metabolism77134059490.20
ko04911Insulin secretion37131359490.20
ko00250Alanine, aspartate and glutamate metabolism37131359490.20
ko04612Antigen processing and presentation37131359490.20
ko04623Cytosolic DNA-sensing pathway2713759490.20
ko03320PPAR signaling pathway47132059490.21
ko03440Homologous recombination47132059490.21
ko04141Protein processing in endoplasmic reticulum2371316159490.21
ko05223Non-small cell lung cancer1713259490.23
ko04916Melanogenesis1713259490.23
ko00053Ascorbate and aldarate metabolism|00562:Inositol phosphate metabolism1713259490.23
ko05012Parkinson's disease2713859490.25
ko03430Mismatch repair2713859490.25
ko03460Fanconi anemia pathway67133659490.26
ko04152AMPK signaling pathway57132959490.26
ko00910Nitrogen metabolism37131559490.26
ko00051Fructose and mannose metabolism37131559490.26
ko00514Other types of O-glycan biosynthesis47132259490.27
ko00130Ubiquinone and other terpenoid-quinone biosynthesis2713959490.29
ko00260Glycine, serine and threonine metabolism37131659490.30
ko04972Pancreatic secretion37131659490.30
ko02010ABC transporters77134659490.31
ko04360Axon guidance117137759490.31
ko00785Lipoic acid metabolism1713359490.32
ko04932Non-alcoholic fatty liver disease (NAFLD)1713359490.32
ko05169Epstein-Barr virus infection1713359490.32
ko04330Notch signaling pathway67133959490.32
ko00534Glycosaminoglycan biosynthesis - heparan sulfate / heparin37131759490.33
ko04970Salivary secretion37131859490.37
ko04110Cell cycle77134959490.37
ko04620Toll-like receptor signaling pathway27131159490.39
ko00630Glyoxylate and dicarboxylate metabolism27131159490.39
ko00511Other glycan degradation27131159490.39
ko03018RNA degradation87135859490.39
ko00603Glycosphingolipid biosynthesis - globo series1713459490.40
ko04940Type I diabetes mellitus1713459490.40
ko04270Vascular smooth muscle contraction27131259490.43
ko05110Vibrio cholerae infection1713559490.47
ko04973Carbohydrate digestion and absorption1713559490.47
ko012102-Oxocarboxylic acid metabolism|01230:Biosynthesis of amino acids|00330:Arginine and proline metabolism1713559490.47
ko00071Fatty acid degradation1713559490.47
ko00970Aminoacyl-tRNA biosynthesis57133859490.49
ko04014Ras signaling pathway2671321459490.50
ko00790Folate biosynthesis27131459490.51
ko04962Vasopressin-regulated water reabsorption27131459490.51
ko04975Fat digestion and absorption1713659490.54
ko04723Retrograde endocannabinoid signaling1713659490.54
ko00750Vitamin B6 metabolism1713659490.54
ko05132Salmonella infection1713659490.54
ko03008Ribosome biogenesis in eukaryotes87136659490.54
ko00561Glycerolipid metabolism67134959490.54
ko00040Pentose and glucuronate interconversions27131559490.55
ko04146Peroxisome57134159490.56
ko05206MicroRNAs in cancer47133359490.57
ko05014Amyotrophic lateral sclerosis (ALS)1713759490.59
ko04550Signaling pathways regulating pluripotency of stem cells47133459490.59
ko05166HTLV-I infection27131759490.62
ko04742Taste transduction27131759490.62
ko00604Glycosphingolipid biosynthesis - ganglio series1713859490.64
ko04919Thyroid hormone signaling pathway37132759490.64
ko04020Calcium signaling pathway117139959490.65
ko00280Valine, leucine and isoleucine degradation27131859490.65
ko05202Transcriptional misregulation in cancers107139159490.66
ko04015Rap1 signaling pathway107139259490.68
ko00860Porphyrin and chlorophyll metabolism27131959490.68
ko00450Selenocompound metabolism1713959490.68
ko05162Measles1713959490.68
ko00670One carbon pool by folate1713959490.68
ko00140Steroid hormone biosynthesis37133059490.72
ko04144Endocytosis1571314059490.72
ko00920Sulfur metabolism17131059490.72

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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