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Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

James C Costello12, Mehmet M Dalkilic13, Scott M Beason1, Jeff R Gehlhausen1, Rupali Patwardhan34, Sumit Middha35, Brian D Eads2 and Justen R Andrews12*

Author Affiliations

1 School of Informatics, Indiana University, E. Tenth St, Bloomington, Indiana 47408, USA

2 Department of Biology, Indiana University, E. Third St, Bloomington, Indiana 47405, USA

3 Center for Genomics and Bioinformatics, Indiana University, E. Third St., Bloomington, Indiana 47405, USA

4 Current address: Department of Genome Sciences, University of Washington, NE Pacific St, Seattle, Washington 98195-5065, USA

5 Current address: Bioinformatics Core, Mayo Clinic, First St SW, Rochester, Minnesota 55905, USA

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Genome Biology 2009, 10:R97  doi:10.1186/gb-2009-10-9-r97

Published: 16 September 2009

Additional files

Additional data file 1:

The matrix contains GO:BP terms by dataset with the P-value reported in each cell.

Format: TXT Size: 395KB Download file

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Additional data file 2:

All predictions meet the criteria of tp ≥ 0.1.

Format: XLS Size: 4MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional data file 3:

All predictions meet the criteria of tp ≥ 0.1.

Format: XLS Size: 9.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional data file 4:

In addition to gene-GO:BP predictions, the file also contains all GO annotations from v5.3 and v5.7 of the D. melanogaster genome, best blast hits to the NCBI nr database, and any GO annotations transferred to the gene based on sequence similarity. Genes having any evidence supporting the GO:BP prediction are marked.

Format: XLS Size: 556KB Download file

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Additional data file 5:

A set of signal recognition particle (SRP)-related genes were taken from Teleman et al. [79] and a network was built around this query set of genes from the connections in . This file contains information related to gene expression, GO terms, and notes on whether a gene is related to the protein secretory pathway. Networks and along with the full set of functional relationships between Drosophila gene pairs are made available at [48].

Format: XLS Size: 111KB Download file

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Open Data