MiRaGE: Inference of gene expression regulation via microRNA transfection II
MiRaGE: Inference of gene expression regulation via microRNA transfection II Yh. Taguchi/Dept.Phys.,Chuo Univ.Jun Yasuda /School Med.,Tohoku Uinv.
MiRaGE:MiRNA Ranking by Gene ExpressionWhat is miRNA?noncoding RNAs which bind to mRNAs and cleavage them or disturb translation.
Regulation of gene expression via miRNA Computer oriented prediction (uncertain) Target genes genome microRNA mRNA microRNA mRNA 3
miRNA target gene list Gene8 Gene7 Gene6 Gene5 Gene4 Gene3 Gene2 Gene1simple seed match(Virtual) miRNA1 ○×○○○○×× miRNA2 ○×○○××○○Prediction miRNA3 ×○○×○○×× miRNA4 ○○○×○○×× VS Human lung cancer gene1 gene2 miRNA1 Real gene3 4
Concepts of MiRaGE method Control Treated All ofmiRNAs Gene target Expression Gather the information of miRNAs targets Compare the expressions of targets for each miRNAs and check significance (see Next Slides) Calculate False Discovery Rate 5 Generate ranking of each miRNA
Computation of significance miRNA Targets Down Pvalue FDR miRa 54 3 0.5 0.41st miRb 120 54 0.0001 0.005 miRc 36 1 0.5 0.7 ... ... ... ... ...2nd miRX 60 18 0.001 0.007 Reject miRa & c because the FDR > 0.05 Ranking 6
ApplicationInference of transfection of miRNA to human lung cancer cell
Gene expression byArray: AgilentatOne and three days after transfection ofMir107, mir185, and let7a.log(xg[miRNA]) vs log(xg[Control]) xg: gene expressionTarget gene list: simple seed match ICIC2011, LNBI in press. (2011/8/1114)
Transfected miRNA mir107 mir185 let7atime replicate 1 replicate 2 replicate 1 replicate 2 replicate 1 replicate 2day1 1[1st] 1[1st] 7[1st] 9[1st] 2[1st] 2[1st]day3 1[1st] 0 0[1st] 0 1[1st] 1[1st]Numbers of significant miRNAs. The ranks of transfected micriRNAs are shown in square brackets. Transfected miRNAs are correctly identified by MiRaGE method.
ConclusionMiRaGE method can correctly infer regulation of miRNA vis target mRNA expression.The application is now planed...
Web Serverhttp://granular.com/MiRaGE/ now availableData basehttp://granular.com/MiRaGEDB/Collection of results by MiRaGE to GEO(Gene expression Omnibus)coming soon...