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

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

Tohoku Medical Megabank Organization (ToMMo)

Research output: Contribution to journal › Article › peer-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 language	English
Pages (from-to)	212-221
Number of pages	10
Journal	Genome informatics. International Conference on Genome Informatics
Volume	20
Publication status	Published - 2008

ASJC Scopus subject areas

Medicine(all)

Cite this

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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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T1 - A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.

AU - Hatanaka, Yosuke

AU - Nagasaki, Masao

AU - Yamaguchi, Rui

AU - Obayashi, Takeshi

AU - Numata, Kazuyuki

AU - Fujita, Andrè

AU - Shimamura, Teppei

AU - Tamada, Yoshinori

AU - Imoto, Seiya

AU - Kinoshita, Kengo

AU - Nakai, Kenta

AU - Miyano, Satoru

PY - 2008

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

Abstract

ASJC Scopus subject areas

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