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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

Stewart MacArthur16, Xiao-Yong Li12, Jingyi Li3, James B Brown3, Hou Cheng Chu1, Lucy Zeng1, Brandi P Grondona1, Aaron Hechmer1, Lisa Simirenko1, Soile VE Keränen1, David W Knowles4, Mark Stapleton1, Peter Bickel3, Mark D Biggin1* and Michael B Eisen125*

Author Affiliations

1 Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84-181, Berkeley, CA 94720, USA

2 Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA

3 Department of Statistics, University of California Berkeley, Berkeley, CA 94720, USA

4 Life Sciences Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84-181, Berkeley, CA 94720, USA

5 Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA

6 Current address: Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

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Genome Biology 2009, 10:R80  doi:10.1186/gb-2009-10-7-r80

Published: 23 July 2009

Additional files

Additional data file 1:

The antibodies used specifically recognize the transcription factors they were raised against in the embryo.

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Additional data file 2:

See Table 2, Li et al. [11], and Materials and methods for further details.

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Additional data file 3:

These are plotted down the ChIP/chip rank list in non-overlapping 200-peak cohorts.

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Additional data file 4:

The top 200 ChIP/chip peaks are significantly enriched over all peaks in the 1% FDR set for the values plotted in Figures 2, 5, 6 and 8.

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Additional data file 5:

Relative levels of mean UV crosslinking and mean ChIP/chip scores across a series of highly and poorly bound genomic regions.

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Additional data file 6:

Genomic coordinates of regions bound by each factor for the 1% FDR data set, locations and scores of peak windows, and the closest gene and closest transcribed gene for each peak.

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Additional data file 7:

Genomic coordinates of regions bound by each factor for the 25% FDR data set, locations and scores of peak windows, and the closest gene and closest transcribed gene for each peak.

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Additional data file 8:

Fraction of bound regions in different cohorts distinguished by ChIP/chip score and, for some factors, the fraction of those bound regions that overlap known CRMs, using the conventions shown in Figure 4.

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Additional data file 9:

These are shown plotted down the ChIP/chip rank list in non-overlapping 200-peak cohorts.

Format: PDF Size: 2.6MB Download file

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Additional data file 10:

These are plotted down the ChIP/chip rank list in non-overlapping 200-peak cohorts.

Format: PDF Size: 2.9MB Download file

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Additional data file 11:

These are plotted down the ChIP/chip rank list in non-overlapping 200-peak cohorts.

Format: PDF Size: 4.2MB Download file

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Additional data file 12:

These are plotted down the ChIP/chip rank list in non-overlapping 200-peak cohorts.

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Additional data file 13:

Values plotted in the heat maps in Figures 9, 12 and 13, percentages of the top 300 1% FDR peaks bound by 1, 8 or more, 15 or more or 21 factors, and the results of Mann-Whitney tests applied to the data in Figures 12 and 13.

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Additional data file 14:

The pattern of ChIP/chip scores on the eve gene for both factor and negative control immunoprecipitations for all antibodies shown in Table 2.

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