A Novel Strategy to Search Conserved Transcription Factor Binding Sites among Coexpressing Genes in Human

Yosuke Hatanaka (hatanaka@hgc.jp)
Masao Nagasaki (masao@ims.u-tokyo.ac.jp)
Rui Yamaguchi (ruiy@ims.u-tokyo.ac.jp)
Takeshi Obayashi (obayashi@hgc.jp)
Kazuyuki Numata (numata@ims.u-tokyo.ac.jp)
André Fujita (afujita@ims.u-tokyo.ac.jp)
Teppei Shimamura (shima@ims.u-tokyo.ac.jp)
Yoshinori Tamada (tamada@ims.u-tokyo.ac.jp)
Seiya Imoto (imoto@ims.u-tokyo.ac.jp)
Kengo Kinoshita (kino@ims.u-tokyo.ac.jp)
Kenta Nakai (knakai@ims.u-tokyo.ac.jp)
Satoru Miyano (miyano@ims.u-tokyo.ac.jp)

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan


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.

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Japanese Society for Bioinformatics