Research article
A global analysis of genetic interactions in Caenorhabditis elegans
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
Journal of Biology 2007, 6:8 doi:10.1186/jbiol58
Published: 26 September 2007Additional 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].
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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.
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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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