High throughput data sets from DNA, RNA and protein assays are abundant and will only become more prevalent in the near future. When combined with knowledge from decades of detailed genetic investigations linking individual genes to phenotypes, these datasets offer genome-wide insights into the functional relationship among genes. However, questions still arise regarding the feasibility of integrating these disparate data sets. Our goal is to demonstrate that by adopting a probabilistic framework, the large and diverse data sets acquired from studies of a complex metazoan can be integrated to provide a meaningful, functional gene network and to draw new and unforeseen connections.
The contents of this page are supplemental data to Gene Networks in Drosophila melanogaster: Integrating experimental data to predict gene function Genome Biology 10(9) 2009 Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function.
- Supplemental Figures and Tables
- Matrix of p-values for used to construct the GO term vs. Dataset image
- GO term vs. Datasets (Additional data file 1)
- Network constructed from top 20,000 gene pairs. Formatted as a Cytoscape .cys session file. The session contains the network laid out with nodes labeled with gene names and the top 20 gene clusters identified through the MCODE plug-in. Extensive documentation is provided through the cytoscape.org website. Right-clicking on any node will bring up a menu that provides a link-out to FlyBase.
- 20k network.cys
- Launch network in Cytoscape using Java Webstart (Click Cytoscape logo)
readme - Network constructed from top 200,000 gene pairs. Formatted as a Cytoscape .cys session file. The session contains the network laid out with nodes labeled with gene names and the top 20 gene clusters identified through the MCODE plug-in. Extensive documentation is provided through the cytoscape.org website. Right-clicking on any node will bring up a menu that provides a link-out to FlyBase.
- 200k network.cys
- Launch network in Cytoscape using Java Webstart (Click Cytoscape logo)
readme - The full set of 25 million relationships and the corresponding log-likelihood scores for each dataset.
- GO biological process predictions using the Markov random field method and the network with 20k gene pairs.
- 20k predictions (Additional File 2)
- GO biological process predictions using the Markov random field method and the network with 200k gene pairs.
- 200k predictions (Additional File 3)
- GO biological process predictions using the Markov random field method and the network with 20k gene pairs. These predictions have been filtered to 424 genes.
- Analysis of predictions on 483 genes (Additional File 4)
- Annotation of the 70 gene network cluster of signal recognition particle (SRP)-related genes.
- SRP-related network information (Additional File 5)

