As the ‘histone code’ hypothesis gains steam, it’s become obvious that there isn’t much out there to help the chromatin research community look for combinatorial relationships between histone modifications. That’s where the Coherent and Shifted Bicluster Identification (CoSBI) algorithm comes in; to help wring even more data from genome wide histone mod maps.
Not to be confused with the beloved, bad sweater wearing comedian (see Cosby, Bill), CosBI identifies recurrent combinatorial chromatin modifications across a given epigenome…something other tools can’t do. “Current main stream analysis tools only look at one or two chromatin maps at a time. In most studies, data integration comes in as a post-processing step. The field really lacks tools for integrative analysis of multiple chromatin modification maps. That’s the motivation for our new tool.” explains Kai Tan who helped engineer CoSBI at the Universtiy of Iowa.
The Iowa scientists gave their new subspace clustering algorithm a test run on a set of 39 chromatin modifaction maps from human T cells, where they uncovered:
- 843 different combinatorial patterns that pop up in over 0.1% of the genome
- 19 distinct chromatn mods, 10 of which show up in more than half of the patterns
- Combinatorial signatures for 8 classes of functional DNA elements
The CoSBI kids hope their newest creation will become a hit in chromatin research circles. “With the rapid increase in genome-wide chromatin modification maps, application of our tool will aid data interpretation and generation of novel insights into epigenetic regulation of gene expression.” says Tan.
Learn more about what makes CoSBI tick at Nucleic Acids Research, January 2011 or check out the Tan Lab Home Page and try it our for yourself.