Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines.
Microribonucleic acids (miRNAs) are small noncoding RNAs that negatively regulate gene expression at the posttranscriptional level. Although considerable progress has been made in studying the function of miRNAs, they still remain largely unclear, mainly because of the difficulty in identifying target genes for miRNA. We performed a global analysis of both miRNAs and mRNAs expression across 16 human cell lines and extracted negatively correlated pairs of miRNA and mRNA which indicate miRNA-target relationship. The many of known-target of miR-124a showed negative correlation, suggesting our analysis were valid. We further extracted physically relevant miRNA-target gene pairs, applying computational target prediction algorithm with inverse correlations of miRNA and messenger RNA (mRNA) expression. Furthermore, gene-ontology-based annotation and functional enrichment analysis of the extracted miRNA-target gene pairs made it possible to indicate putative functions of miRNAs. The data collected here will be of value for further studies into the function of miRNA.
Ruike
Yoshinao
Y
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho Sakyo-ku, Kyoto, 606-8501, Japan.
Ichimura
Atsuhiko
A
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho Sakyo-ku, Kyoto, 606-8501, Japan.
Tsuchiya
Soken
S
Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Shimizu
Kazuharu
K
Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Kunimoto
Ryo
R
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho Sakyo-ku, Kyoto, 606-8501, Japan.
Okuno
Yasushi
Y
Department of Pharmacoinformatics, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Tsujimoto
Gozoh
G
Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho Sakyo-ku, Kyoto, 606-8501, Japan. gtsuji@pharm.kyoto-u.ac.jp.
D000465:Algorithms; D001483:Base Sequence; D002460:Cell Line; D017931:DNA Primers / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
D017931:DNA Primers; D035683:MicroRNAs; D012333:RNA, Messenger