Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines

Yoshinao Ruike, Atsuhiko Ichimura, Soken Tsuchiya, Kazuharu Shimizu, Ryo Kunimoto, Yasushi Okuno, Gozoh Tsujimoto

Research output: Contribution to journalArticlepeer-review

73 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)515-523
Number of pages9
JournalJournal of Human Genetics
Issue number6
Publication statusPublished - 2008 Jun


  • Correlation analysis
  • GO analysis
  • Micro-RNA
  • Microarray
  • Transcriptome

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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