Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2011 Dec 1;27(23):3319-20. doi: 10.1093/bioinformatics/btr567. Epub 2011 Oct 12.

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis.

Author information

1
Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA. s.kumar@asu.edu

Abstract

SUMMARY:

Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.

AVAILABILITY:

http://www.flyexpress.net

CONTACT:

s.kumar@asu.edu.

PMID:
21994220
PMCID:
PMC3223365
DOI:
10.1093/bioinformatics/btr567
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center