GExplore ...
... is a tool for large-scale mining of data related to gene or protein function in C. elegans. The interface is simple and response times are fast to encourage large-scale exploratory searches. The database contains selected genome-wide data sets including protein domain organisation, gene expression and phenotype data, which are important indicators for gene and protein function. Data sets were obtained from Wormbase and processed to integrate data and to simplify searches.
This site should be useful for experimental planning of genome-scale experiments and survey-type queries. With this interface you should be able to get quick answers to questions such as:
- How many small secreted proteins are there?
- Which putative cell surface receptors are expressed in neurons?
- How many kinases expressed in muscle cells have mutants available?
GExplore version 1.4 is a major update including the following novel data sets and features:
- all databases were updated to Wormbase release 250
- the domain organization for the proteomes of all nine core species in Wormbase was added to allow searches for proteins with certain domains in different nematode species
- gene ontology data were added for all species
- the location of C. elegans mutations was mapped onto the domain organization of the proteins
- SAGE and RNAseq expression data were replaced by new stage-specific expression profiles from the modENCODE project (provided by the Waterston lab)
- best BLAST hits were replaced by orthologs as listed by Wormbase; a search option to identify C. elegans orthologs of human, mouse, Drosophila or yeast genes was added
The previous GExplore database version 1.3 is available here.
The Individual Search Pages
Proteins
Search for proteins with certain domains or domain arrangements. Allows sophisticated domain patterns searches like 'one or more immunoglobulin domains followed by 3-5 fibronectin III domains followed by a single transmembrane domain'. The database contains protein data (wormbase release 250) for the follwoing species: C. elegans, C. briggsae, C. remanei, C. brenneri, C. japonica, P. pacificus, B. malayi, O. volvulus and S. ratti
Mutations
Search interface to display the location of mutations in C. elegans genes mapped onto the domain organization of the protein. Can be used to identify mutations affecting particular protein domains or splice variants.
Genes
Interface to search for and display domain organization, phenotype, expression, Gene Ontology terms, orthologs and map position of C. elegans genes.
Expression
Interface to search for stage-specific expression profiles of C. elegans genes. Quantitative data are avialable from RNAseq experiments for 18 embryonic stages and all postembryonic stages.
Compare
A simple interface comparing two sets of genes to identify common and unique genes in the sets.
How to cite GExplore
The publication describing the first version is:
Hutter H, Ng MP, Chen N.
GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes.
BMC Genomics. 2009 Nov 16;10:529.
A manuscript describing the new version is in preparation.