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.
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
Additional Data File 3.
Networks created for this study (XLS, 8 Mb).
Gene interactions in the SGI,
Query, and Superimposed networks.
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.
Data File 5. The
SGI interactions are synthetic (DOC, 45 Kb). A
detailed assessment of the nature of the SGI interactions is presented.
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
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
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
Additional Data File 9.
Subnetworks and Broad Subnetworks (XLS, 138 Kb).
Genes and functional
annotations for all subnetworks.
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.
File 11. Comparison
of bridging propensities among high throughput datasets (DOC, 32 Kb). The
bridging propensity of various datatypes is represented.
File 12. Functional annotation (Gzipped
TXT, 28 Mb). All functional
categories and their associated genes are listed.
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.
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.