BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions

Chicco D, Bi HS, Reimand J, Hoffman MM. 2018. BEHST – Genomic set enrichment analysis enhanced through integration of chromatin long-range interactions. In preparation.

The free BEHST software package efficiently associates functional enriched Gene Ontology terms to input genomic regions

BEHST reads a dataset of genomic regions, and intersects them with the chromatin interactions available in the Hi-C dataset (Rao et al, Cell, 2014). Of these genomic regions, BEHST selects those that are present in the regulatory regions of genes a dataset of principal isoform annotations. We defined these cis-regulatory regions upon the position of their nearest transcription start site of the genes' principal transcripts, plus an upstream and downstream extension. Afterwards, BEHST selects the genes of the resulting partner loci found in gene regulatory regions, and inserts them into g:Profiler. BEHST, finally, produces the list of the most significant Gene Ontology terms detected by g:Profiler.

Web application

The web application of BEHST is publically available on behst.hoffmanlab.org

Installation

BEHST can run on any Linux and Mac computers. You can find the installation instructions on the BEHST Bitbucket webpage.

Source code

You can find the source code repository on the BEHST Bitbucket webpage.

Support

For support of BEHST, please write to the BEHST-users mailing list, rather than writing the authors directly. Using the mailing list will get your question answered more quickly. It also allows us to pool knowledge and reduce getting the same inquiries over and over. Questions sent to the mailing list will receive a higher priority than those sent to us individually.

If you do not want to read discussions about other people's use of BEHST, but would like to hear about new releases and other important information, please subscribe to the BEHST-announce mailing list mailing list.

Credits

BEHST was developed by Davide Chicco, Haixin Sarah Bi, Juri Reimand, and Michael M. Hoffman at the Hoffman Lab of the Princess Margaret Cancer Centre (Toronto, Ontario, Canada).