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Byrne AB
Weirauch MT
Wong V
Koeva M
Dixon SJ
Stuart JM
Roy PJ

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Koeva M
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Stuart JM
Roy PJ
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Research article

A global analysis of genetic interactions in Caenorhabditis elegans

Alexandra B Byrne¹^,2 , Matthew T Weirauch³ , Victoria Wong¹ , Martina Koeva³ , Scott J Dixon¹^,2 , Joshua M Stuart³ and Peter J Roy¹^,2

¹Department 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

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

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

author email corresponding author email

Journal of Biology 2007, 6:8doi: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.

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Additional data file 2:

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

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Additional data file 3:

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

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Additional data file 4:

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

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Additional data file 5:

A detailed assessment of the nature of the SGI interactions.

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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).

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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

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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.

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Additional data file 9:

Genes and functional annotations for all subnetworks.

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Additional data file 10:

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

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Additional data file 11:

The bridging propensity of various data types is represented.

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Additional data file 12:

All functional categories and their associated genes are listed.

Format: GZ Size: 4MB Download file

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.

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Additional data file 14:

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

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