A Global Analysis of Genetic Interactions

in Caenorhabditis elegans

 

 

All Additional Data Files  (6.2 Mb, zipped)  

 

Additional Data File 1.  SGI Growth Matrix (XLS, 202 Kb).  Average growth scores for each query; target pair tested in the SGI analysis are presented in tabular form.  Enhancing (E) and alleviating (A) interactions are also indicated. 

Additional Data File 2.  Distribution of Functional Categories within the LGIII set (XLS, 71 Kb).  The LG III target genes were analysed for enrichment of specific GO annotation.

Additional Data File 3.  Networks created for this study (XLS, 8 Mb).  Gene interactions in the SGI, Query, and Superimposed networks.

Additional Data File 4.   Sorted list of interactions based on interaction strength (XLS, 0.98 Mb).  Average interaction strengths for each query; target pair tested are listed in tabular form.

Additional Data File 5.  The SGI interactions are synthetic (DOC, 45 Kb). A detailed assessment of the nature of the SGI interactions is presented.

Additional Data File 6.  Reciprocal Query-Query Interactions (DOC, 32 Kb).  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).

Additional Data File 7.  Clustered table of growth scores (XLS, 384 Kb).  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] .

Additional Data File 8.  Multiply Supported Subnetworks are Enriched for Genes with Similar GO Annotations (DOC, 131 Kb).  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.

Additional Data File 9.  Subnetworks and Broad Subnetworks (XLS, 138 Kb).  Genes and functional annotations for all subnetworks.

Additional Data File 10.  Subnetworks are significantly bridged by SGI links (DOC, 55 Kb).  33 focused subnetwork pairs are listed along with the corresponding enrichment of SGI links that bridge them. 

Additional Data File 11.  Comparison of bridging propensities among high throughput datasets (DOC, 32 Kb).  The bridging propensity of various datatypes is represented.

Additional Data File 12.  Functional annotation (Gzipped TXT, 28 Mb).  All functional categories and their associated genes are listed.

Additional Data File 13.  The LOFA is superior to PCC at predicting genes of related function (DOC, 29 Kb).  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.

Additional Data File 14.  Normal Approximation in Z-transformation (DOC, 131 Kb).  Evidence supporting the validity of using a normal approximation in the Z-transformation to estimate bridging significance is presented.