Defining Transcriptional Networks through Integrative Modeling of mRNA Expression and Transcription Factor Binding Data Analysis of Functional Transcription Binding in Yeast

Feng Gao, Barrett C. Foat and Harmen J. Bussemaker*

Department of Biological Sciences, Columbia University, New York, NY 10027, and *Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032

BMC Bioinformatics 2004, 5:31 (published 18 March 2004)

Figures and Tables

Figure 1. Overview of our method for determining regulatory coupling strengths between transcription factors and their putative target genes.

Figure 2. Enrichment for functional annotation

Figure 3. Assigning directionality to divergently transcribed promoters.

Table 1: Classification of genes according to ChIP data and inferred regulatory coupling.

Table 2: Analysis of transcription response to transcription factor deletion.

Table 3: Overrepresentation of four cell cycle-related motifs.

Table 4: Replacing regulatory coupling strength by transcription factor deletion data

Supplementary Material

1. Information of gene expression dataset

2. Gene list of B+/C+ and B+/C- groups for each transcription factor

3. Over-represented GO categories for each transcription factor

Download Material

Download transcription factor activity profile (TFAP) -- t value (text format)

Download transcription factor activity profile (TFAP) -- p value (text format)

Download binding and coupling results (text format)

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