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Bioinformatics. 2011 Jun 1;27(11):1589-90. doi: 10.1093/bioinformatics/btr185. Epub 2011 Apr 19.

VIZ-GRAIL: visualizing functional connections across disease loci.

Author information

1
Divisions of Genetics and Rheumatology, Brigham and Women's Hospital, Boston, MA 02115, USA. soumya@broadinstitute.org

Abstract

MOTIVATION:

As disease loci are rapidly discovered, an emerging challenge is to identify common pathways and biological functionality across loci. Such pathways might point to potential disease mechanisms. One strategy is to look for functionally related or interacting genes across genetic loci. Previously, we defined a statistical strategy, Gene Relationships Across Implicated Loci (GRAIL), to identify whether pair-wise gene relationships defined using PubMed text similarity are enriched across loci. Here, we have implemented VIZ-GRAIL, a software tool to display those relationships and to depict the underlying biological patterns.

RESULTS:

Our tool can seamlessly interact with the GRAIL web site to obtain the results of analyses and create easy to read visual displays. To most clearly display results, VIZ-GRAIL arranges genes and genetic loci to minimize intersecting pair-wise gene connections. VIZ-GRAIL can be easily applied to other types of functional connections, beyond those from GRAIL. This method should help investigators appreciate the presence of potentially important common functions across loci.

AVAILABILITY:

The GRAIL algorithm is implemented online at http://www.broadinstitute.org/mpg/grail/grail.php. VIZ-GRAIL source-code is at http://www.broadinstitute.org/mpg/grail/vizgrail.html.

PMID:
21505031
PMCID:
PMC3102227
DOI:
10.1093/bioinformatics/btr185
[Indexed for MEDLINE]
Free PMC Article

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