CMGSDB -- integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
What you can do:
The Database for Computational Modeling of Gene Silencing is an integration of heterogeneous data sources about C. elegans with capabilities for compositional data mining across diverse domains.
Highlights:
- Besides gene, protein, and functional annotations, CMGSDB currently unifies information about 531 RNAi phenotypes obtained from heterogeneous databases using a hierarchical scheme.
- A phenotype browser at the CMGSDB website serves this hierarchy and relates phenotypes to other biological entities.
- The application of CDM to CMGSDB produces 'chains' of relationships in the data by finding two-way connections between sets of biological entities.
- Chains can, for example, relate the knock down of a set of genes during an RNAi experiment to the disruption of a pathway or specific gene expression through another set of genes not directly related to the former set.
- CMGSDB contains details of genome annotation data (chromosomes, genes, coding transcripts), protein structure data (secondary structure, physical properties), microarray expression data (genomewide gene expressions for over 500 microarray experiments), RNA interferance data (RNAi experiment details, phenotypes exhibited by genes in different experiments, phenotype hierarchy and associations between them), protein-protein interaction data, and gene-regulation data.
Keywords:
- RNAi
- RNA interference
- c. elegans
- Caenorhabditis elegans RNA interference
- cell-based phenotypes
- gene silencing
- data mining
Literature & Tutorials:
This record last updated: 02-20-2008