Online Motif Discovery

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Duncan T. Odom, Robin D. Dowell, Elizabeth S. Jacobsen,
William Gordon, Timothy W. Danford, Kenzie D. MacIsaac,
P. Alexander Rolfe, Caitlin M. Conboy, David K. Gifford and Ernest Fraenkel

Supplementary data for Nature Genetics 39, 730 - 732 (2007)

Lists of peaks used in the paper

Click here to download lists of the binding events that were considered signficant at the default cutoffs used in the paper.
Explanation of file format
There are two files, one for human and one for mouse. Each file is a concatenation of the four transcription factors (FOXA2, HNF1A, HNF4A, HNF6) for each species. Each peak list begins with a descriptor line. For example:
---Hs FOXA2:liver:tissue vs WCE:liver:tissue;HC:median
indicates that the data which follows is from Human FOXA2.
Each subsequent line consists of:
TSSid \t #peaks [\t location \t score \t confidence]
TSSid is an identifier of the form refseqid:chromosome:start which is unique to each transcription start site (TSS).
#peaks indicates the number of peaks and/or probes associated with this TSS.
This is followed by zero or more peaks (in no particular order), each represented by three fields indicating the location, "score" and "confidence" for each peak. The score is the sum of (posterior*strength) over width of the peak and the confidence is the maximum posterior value within the peak. These values are the direct outputs of JBD (see Qi et al. for more details on the peak calling method). Human genomic coordinates refer to genome version hg17 and mouse coordinates refer to genome version mm6.

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