Biological Enrichment of Hidden Sequence Targets

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.


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



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Source code

BEHST code repository on Bitbucket


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). This website was developed by Abdellatif Daghrach, Dustin Hu, and Kevin Chan of the Princess Margaret Genomics Centre (Toronto, Ontario, Canada).

Upload your files

Query regions

File upload/ URL (.bed)

Optional parameters and files:

Query extension (bp)
Target extension (bp)
Gene annotation (.gtf)

Chromosomal interactions (.hiccups)

Principal transcripts (.bed)