A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.

Yosuke Hatanaka, Masao Nagasaki, Rui Yamaguchi, Takeshi Obayashi, Kazuyuki Numata, Andrè Fujita, Teppei Shimamura, Yoshinori Tamada, Seiya Imoto, Kengo Kinoshita, Kenta Nakai, Satoru Miyano

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

We report various transcription factor binding sites (TFBSs) conserved among co-expressed genes in human promoter region using expression and genomic data. Assuming similar promoter structure induces similar transcriptional regulation, hence induces similar expression profile, we compared the promoter structure similarities between co-expressed genes. Comprehensive TF binding site predictions for all human genes were conducted for 19,777 promoter regions around the transcription start site (TSS) given from DBTSS and promoter similarity search were conducted among coexpressing genes data provided from newly developed COXPRESdb. Combination of Position Weight Matrix (PWM) motif prediction and bootstrap method, 7,313 genes have at least one statistically significant conserved TFBS. We also applied basket method analysis for seeking combinatorial activities of those conserved TFBSs.

Original languageEnglish
Pages (from-to)212-221
Number of pages10
JournalGenome informatics. International Conference on Genome Informatics
Volume20
Publication statusPublished - 2008

ASJC Scopus subject areas

  • Medicine(all)

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