Research
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
- † Equal contributors
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
Genome Biology 2009, 10:R80 doi:10.1186/gb-2009-10-7-r80
Published: 23 July 2009Additional 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.
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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
This file can be viewed with: Adobe Acrobat Reader
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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