miRFocus for Integration of miRNAome and Proteome Analysis
Recent development of clinical technologies has put a focus on pathway-based integrated analysis of cellular proteins and regulation of gene expression.
miRFocus was developed to help researchers save valuable time in information mining once microRNA (miRNA) expression data are obtained by providing leads for in-depth analysis of miRNA-target gene pathways and the related miRNA annotations.
Figure 1 – miRFocus input example – http://mirfocus.org/
MicroRNAs (miRNAs) are short regulatory ribonucleic acid (RNA) molecules, which consist of about 20-23 nucleotides and are found in all eukaryotic cells. miRNAs play important roles as translational and post-transcriptional regulators by binding to complementary sequences of the target messenger RNA transcripts (mRNAs), such interactions usually resulting in gene silencing due to translational repression.
MiRNAs have now been accepted as effective molecular signatures of disease diagnosis, specifically cancers, which still remain a major threat for human vitality. Abundant information exists linking signature miRNAs with a particular cancer or a subtype of a cancer1.
miRFocus is a new web resource, which promises to provide cancer biomarker miRNAs for cancer screening. miRFocus can be utilized for pathway analysis and identification of specific miRNAs as reporters of tumor genesis pathways. This method has great potential in defining a molecular diagnostic (MDx or miRDx) panel for population-based preventive examination of cancer occurrences.
Expression profiling by LC Sciences’ miRNA microarray service revealed a list of differentially expressed miRNAs. Those miRNAs are then input into the miRFocus web portal for analysis of:
miRNA Basic Information(miRBase)
· Gene Family
· Gene Cluster
Other Related Databases
· Journal, abstract & citation
Target Gene (miRecords)
· Interaction of miRNA and target gene
· Gene Ontology
Figure 2 – miRFocus output example – http://mirfocus.org/
These pathway biomarker miRNAs lead to protein candidate markers that are detected can be investigated by LC Sciences’ proteomic PepArrays™. Whole cancer cell lysate analysis on the PepArrays™ specifically designed to assay the pathway reporter proteins2.
PepArray™ technology involves in situ (on chip) high density peptide synthesis and multiplex protein assays carried out in a microfluidic picoliter scale microarray. The PepArray™ is an assay reaction device which allows thousands of titration reactions, multiple step enzymatic reactions, and other biochemical reactions normally carried out in individual micro tubes or microtiter plates to be performed simultaneously in a single experiment.
1. Youssef YM, White NM, Grigull J, Krizova A, Samy C, Mejia-Guerrero S, Evans A, Yousef GM. (2011) Accurate molecular classification of kidney cancer subtypes using microRNA signature. Eur Urol 59(5), 721-30.
2. LC Sciences’ internal research.