Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

doi:10.1186/1471-2105-9-484

BMC Bioinformatics
Volume 9

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Research article

Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

Jakub Orzechowski Westholm¹ , Feifei Xu¹ , Hans Ronne² and Jan Komorowski¹^,3

¹The Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE-751 24 Uppsala, Sweden

²Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-751 23 Uppsala, Sweden

³Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, 02-106, Warsaw, Poland

author email corresponding author email

BMC Bioinformatics 2008, 9:484doi:10.1186/1471-2105-9-484


Published:	17 November 2008

Additional files

Additional file 1:

Analysis of motif context in promoters bound by transcription factors. The data provided show the results of Context finder for all motif – experiment pairs from the DNA binding data. For each such pair the following values are provided: significance of orientation bias (p-value), significance of location bias (p-value), dispersion and the number of selected promoters. The results in this file are summarized in the first row of Table 1.

Format: XLS Size: 56KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Analysis of motif context in promoters of co-expressed genes. The data provided show the results of Context finder for all motif – experiment pairs from the co-expression data. For each such pair the following values are provided: significance of orientation bias (p-value), significance of location bias (p-value), dispersion and the number of selected promoters. The results in this file are summarized in the third row of Table 1.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Correlation between motif frequency and nucleosome occupancy. The data provided show the correlation between motif frequency and nucleosome occupancy for all motif – experiment pairs from the DNA binding data. The results in this file are summarized in Figure 5b.

Format: XLS Size: 56KB Download file

This file can be viewed with: Microsoft Excel Viewer