Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
Bioinformatics. 2009 Nov 15;25(22):3001-4. Epub 2009 Aug 5.
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks.
Tian F, Shah PK, Liu X, Negre N, Chen J, Karpenko O, White KP, Grossman RL.
School of Medicine, Tsinghua University, Beijing, China 100084.
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. AVAILABILITY: Flynet is available at https://www.cistrack.org/flynet/.
Research Papers
- Sterile alpha motif domain-mediated self-association plays an essential role in modulating the activity of the Drosophila ETS family transcriptional repressor Yan
- Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila
- Novel opportunities for computational biology and sociology in drug discovery
- Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet minipr
- Mutational bias shaping fly copy number variation: implications for genome evolution
- Cleavable C-terminal His-tag vectors for structure determination.
