Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice.

Rui Yamaguchi, Masahiro Yamamoto, Seiya Imoto, Masao Nagasaki, Ryo Yoshida, Kenji Tsuiji, Atsushi Ishige, Hiroaki Asou, Kenji Watanabe, Satoru Miyano

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

We propose an approach to identify activated transcription factors from gene expression data using a statistical test. Applying the method, we can obtain a synoptic map of transcription factor activities which helps us to easily grasp the system's behavior. As a real data analysis, we use a case-control experiment data of mice treated by a drug of Kampo medicine remedying degraded myelin sheath of nerves in central nervous system. Kampo medicine is Japanese traditional herbal medicine. Since the drug is not a single chemical compound but extracts of multiple medicinal herb, the effector sites are possibly multiple. Thus it is hard to understand the action mechanism and the system's behavior by investigating only few highly expressed individual genes. Our method gives summary for the system's behavior with various functional annotations, e.g. TFAs and gene ontology, and thus offer clues to understand it in more holistic manner.

Original languageEnglish
Pages (from-to)119-129
Number of pages11
JournalGenome informatics. International Conference on Genome Informatics
Volume18
Publication statusPublished - 2007
Externally publishedYes

Fingerprint

Kampo Medicine
Transcription Factors
Gene Expression
Gene Ontology
Herbal Medicine
Traditional Medicine
Medicinal Plants
Myelin Sheath
Pharmaceutical Preparations
Central Nervous System
Genes

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice. / Yamaguchi, Rui; Yamamoto, Masahiro; Imoto, Seiya; Nagasaki, Masao; Yoshida, Ryo; Tsuiji, Kenji; Ishige, Atsushi; Asou, Hiroaki; Watanabe, Kenji; Miyano, Satoru.

In: Genome informatics. International Conference on Genome Informatics, Vol. 18, 2007, p. 119-129.

Research output: Contribution to journalArticle

Yamaguchi, R, Yamamoto, M, Imoto, S, Nagasaki, M, Yoshida, R, Tsuiji, K, Ishige, A, Asou, H, Watanabe, K & Miyano, S 2007, 'Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice.', Genome informatics. International Conference on Genome Informatics, vol. 18, pp. 119-129.
Yamaguchi, Rui ; Yamamoto, Masahiro ; Imoto, Seiya ; Nagasaki, Masao ; Yoshida, Ryo ; Tsuiji, Kenji ; Ishige, Atsushi ; Asou, Hiroaki ; Watanabe, Kenji ; Miyano, Satoru. / Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice. In: Genome informatics. International Conference on Genome Informatics. 2007 ; Vol. 18. pp. 119-129.
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