Bioinformatics Advance Access originally published online on August 5, 2009
Bioinformatics 2009 25(22):3001-3004; doi:10.1093/bioinformatics/btp469
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Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
1School of Medicine, Tsinghua University, Beijing, China 100084, 2National Center for Data Mining, University of Illinois at Chicago, MC 249, 851 South Morgan Street, Chicago, IL 60607-7045, 3Institute for Genomics & Systems Biology, The University of Chicago, Cummings Life Sciences Center 431A, 920 East 58th Street, Chicago, IL 60637 and 4Department of Human Genetics and Department of Ecology and Evolution, Cummings Life Sciences Center 5th Floor, 920 East 58th Street, Chicago, IL 60637, USA
*To whom correspondence should be addressed.
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Abstract |
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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{at}uic.edu
Availability: Flynet is available at https://www.cistrack.org/flynet/.
Supplementary information: Supplementary data are available at Bioinformatics online.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Associate Editor: Limsoon Wong
Received on April 30, 2009; revised on July 28, 2009; accepted on July 29, 2009
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