webCAT A web ChIP Association Tester (webCAT)
webCAT allows you to easily compare either
- multiple ChIP peaks from peak-called BED files in a systematic "ChIP versus ChIP" approach.
- multiple ChIP peaks with defined genomic regions (e.g. introns, exons, promoters, intergenic regions, etc...)
Comparison is performed using the Genomic Association Tester framework.
Scores are calculated as: Log2( observed overlap / expected overlap ) x -Log10( p-value )
Peaks that share significantly common genomic binding sites score highly, allowing easy identification of proteins that show similar or identical genomic distributions from those that are distinct.
High genomic association or "co-localisation" between pairs of ChIP data can highlight potential :
- functional complexes or co-factors acting on similar genes.
- antagonistic activators/repressors acting on similar genes.
- preference for a given chromatin-acting protein with one or more histone marks.
- co-occurring histone marks
A note on user-supplied BED files...
- Your BED file must be correctly formatted and the chromosome names be correct for the selected genome - different genome assemblies report chromosome names differently e.g. '1' instead of 'chr1'.
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Due to the time involved in calculating peak association, uploading your own ChIP peak BED file requires the input of a valid email address to which the results will be sent.
To give an example of execution time, each "calculation" takes between 1-4 seconds (depending on server load):- For "ChIP on genomic regions", it takes approximately 3 minutes to score 50 ChIP datasets against 300 genomic regions (50 calculations).
- For "ChIP versus ChIP", it takes approximately 2 hours for comparison of 50 uploaded ChIP BED files (2500 calculations).
- User-supplied Genomic Region BED files are limited to 300 unique region names, as given in the 4th (name) column of the BED file.
- User-supplied ChIP peak BED files are limited to 50 ChIP peak BED files (unlimited regions).
