Open Access Highly Accessed Research article

A global analysis of genetic interactions in Caenorhabditis elegans

Alexandra B Byrne12, Matthew T Weirauch3, Victoria Wong1, Martina Koeva3, Scott J Dixon12, Joshua M Stuart3* and Peter J Roy12*

Author Affiliations

1 Department of Medical Genetics and Microbiology, The Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College St, University of Toronto, Toronto, ON, M5S 3E1, Canada

2 Collaborative Program in Developmental Biology, University of Toronto, Toronto, ON, M5S 3E1, Canada

3 Department of Biomolecular Engineering, 1156 High Street, Mail Stop SOE2, University of California, Santa Cruz, CA 95064, USA

For all author emails, please log on.

Journal of Biology 2007, 6:8  doi:10.1186/jbiol58

Published: 26 September 2007

Additional files

Additional data file 1:

A table presenting average growth scores for each query-target pair tested in the SGI analysis. Enhancing (E) and alleviating (A) interactions are also indicated.

Format: XLS Size: 202KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 2:

LGIII target genes were analyzed for enrichment of specific GO annotation.

Format: XLS Size: 70KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 3:

Gene interactions in the SGI, query, and superimposed networks.

Format: XLS Size: 7.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 4:

Average interaction strengths for each query-target pair tested are listed.

Format: XLS Size: 1008KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 5:

A detailed assessment of the nature of the SGI interactions.

Format: DOC Size: 43KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 6:

Hypomorphic query worms (x-axis) were fed RNAi that targets query genes (y-axis) to measure the reciprocity of SGI. Average growth scores are indicated for each query (mutant); query (RNAi) interaction (E).

Format: DOC Size: 31KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 7:

Targets are included in the table if they interacted with at least one query. Genes are clustered in two dimensions based on the calculated average growth scores. Clusters are labeled A-L and significant enrichment of functional annotation among the genes in each cluster is indicated where applicable (see Materials and methods). Gene function descriptions are from WormBase version 170 [43].

Format: XLS Size: 384KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 8:

MSSNs are listed along with the contributing datasets that make up each MSSN. The amount and significance of GO enrichment among genes of the MSSNs are also indicated.

Format: DOC Size: 115KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 9:

Genes and functional annotations for all subnetworks.

Format: XLS Size: 138KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 10:

33 focused subnetwork pairs are listed along with the corresponding enrichment of SGI links that bridge them.

Format: DOC Size: 51KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 11:

The bridging propensity of various data types is represented.

Format: DOC Size: 32KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 12:

All functional categories and their associated genes are listed.

Format: GZ Size: 3.9MB Download file

Open Data

Additional data file 13:

Precision levels of networks created using various cutoffs of the LOFA and PCC scores are plotted against network size. The arrow indicates the chosen co-phenotype network variant.

Format: DOC Size: 29KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 14:

Evidence supporting the validity of using a normal approximation in the Z-transformation to estimate bridging significance.

Format: DOC Size: 132KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data