Journal Article

Flynet: a genomic resource for <i>Drosophila melanogaster</i> transcriptional regulatory networks

Feng Tian, Parantu K. Shah, Xiangjun Liu, Nicolas Negre, Jia Chen, Oleksiy Karpenko, Kevin P. White and Robert L. Grossman

in Bioinformatics

Volume 25, issue 22, pages 3001-3004
Published in print November 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp469

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Motivation: The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein–DNA interactions and epigenetic marks are becoming available from large projects, such as the model organism ENCyclopedia Of DNA Elements (modENCODE) and from individual labs. Dissemination and visualization of these datasets in an explorable form is an important challenge.

Results: To support research on Drosophila melanogaster transcription regulation and make the genome wide in vivo protein–DNA interactions data available to the scientific community as a whole, we have developed a system called Flynet. Currently, Flynet contains 101 datasets for 38 transcription factors and chromatin regulator proteins in different experimental conditions. These factors exhibit different types of binding profiles ranging from sharp localized peaks to broad binding regions. The protein–DNA interaction data in Flynet was obtained from the analysis of chromatin immunoprecipitation experiments on one color and two color genomic tiling arrays as well as chromatin immunoprecipitation followed by massively parallel sequencing. A web-based interface, integrated with an AJAX based genome browser, has been built for queries and presenting analysis results. Flynet also makes available the cis-regulatory modules reported in literature, known and de novo identified sequence motifs across the genome, and other resources to study gene regulation.

Contact: grossman@uic.edu

Availability: Flynet is available at https://www.cistrack.org/flynet/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  3160 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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