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Prediction of synergistic transcription factors by function conservation

Zihua Hu1*, Boyu Hu2 and James F Collins3

1 Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, Department of Biostatistics, Department of Medicine, University at Buffalo, State University of New York (SUNY), Buffalo, NY 14260, USA

2 Duke University, Durham, NC 27710, USA

3 Department of Exercise and Nutrition Sciences, University at Buffalo, State University of New York (SUNY), Buffalo, NY 14260, USA

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Genome Biology 2007, 8:R257 doi:10.1186/gb-2007-8-12-r257

Published: 5 December 2007

Additional files

Additional data file 1:

Promoter sequences of 1,591 human genes from [58] with at least one E2F1 binding site (PWM: E2F1_Q3_01).

Format: TXT Size: 1.6MB Download file

Open Data

Additional data file 2:

Promoter sequences of 575 human genes from [58] with at least two E2F1 binding sites of between-TFBS distance ≤ 600 bp.

Format: TXT Size: 577KB Download file

Open Data

Additional data file 3:

Promoter sequences within 1 kb upstream of the annotated TSS for the 10,046 human genes.

Format: TXT Size: 9.8MB Download file

Open Data

Additional data file 4:

Promoter sequences within 1 kb upstream of the annotated TSS for the 10,046 mouse genes.

Format: TXT Size: 9.8MB Download file

Open Data

Additional data file 5:

Matrix ID in the TRANSFAC database for the 234 PWMs used in this study.

Format: TXT Size: 3KB Download file

Open Data

Additional data file 6:

PERL scripts for computing TFBS combinations by distance constraints.

Format: TXT Size: 35KB Download file

Open Data