WormNet v. 1 is a probabilistic functional gene network of protein-encoding genes of C. elegans, constructed using a modified Bayesian integration of many different data types from several different organisms, with each data type weighted according to how well it links genes that are known to function together in C. elegans. Each interaction in WormNet has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

To search WormNet please go to the basic search page and enter a gene, or list of genes, in the box provided, using Wormbase public or sequence gene names (e.g. dys-1 or F15D3.1). The search will return all of the genes that are directly connected to an input gene (or set of genes), ranked according to their log-likelihood scores. The evidence for each interaction is indicated using the codes listed at the bottom of this page. WormNet is built on Wormbase release WS140 gene identifiers.

Current network statistics
version# genes# linkagescoverage of WB140 protein-coding loci

A single network comprising the majority of genes accurately predicts the phenotypic effects of gene perturbation in C. elegans
Insuk Lee, Ben Lehner, Catriona Crombie, Wendy Wang, Andrew G. Fraser, and Edward M. Marcotte
Nature Genetics, Vol 40, p181-188 (2008)

Basic search with graph layout
This reports all connected WormNet neighbors to your query genes.
Coherence of query genes is measured by area under the receiver operating characteristic (ROC) curve (AUC) spaning from 0.5 (for no-coherence) to 1 (for maximum-coherence). High AUC (e.g., > 0.65) is considered as predictive. If you see high AUC for genes from your initial screen, their top neighbors would be good candidates for your follow-up screen, network-guided focused screen. This search has seed gene set size limit of 250, and shows graph layouts as well.

Basic search with NO graph layout
Same as above except allowing seeding up to 2,000 genes, but no graph layout

Advanced search
This predicts Gene Ontology (GO) biological process terms for query genes based on WormNet.

Batch download
Benchmark set: WormNet.v1.benchmark.txt (~13MB)
WormNet edges with evidence: WormNet.v1.join.txt (~30MB)
File format: [gene1] [gene2] [CC] [CX] [DM] [GN] [GT] [HS] [PG] [SC] [WI] [IntNet]
CC = Co-citation
CX = Co-expression
DM = fly interologs
GN = Gene neighbors
GT = Genetic interactions
HS = human interologs
PG = Phylogenetic profiling
SC = yeast associalogs
WI = Worm Interactome
IntNet = Integrated network (WormNet)

Questions/Comments: Email: Lee-micro AT mail DOT utexas DOT edu