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CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining.

Pati A, Jin Y, Klage K, Helm RF, Heath LS, Ramakrishnan N - Nucleic Acids Res. (2007)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.

ABSTRACT
CMGSDB (Database for Computational Modeling of Gene Silencing) is an integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains. 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. The web interface for CMGSDB is available at https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/, and serves individual biological entity information as well as details of all chains computed by CDM.

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Related in: MedlinePlus

Screenshot of the gene page.
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Figure 3: Screenshot of the gene page.

Mentions: The web interface of CMGSDB can be used for querying. The user can search against all C. elegans biots. Genes, for example, can be searched using names, loci, transcript IDs and annotations. A biot page, apart from displaying basic information about that biot, also displays relationships with other biots that have been captured within CMGSDB. For instance, the phenotype page not only displays phenotype description, ID and source, but also shows existing relationships with other phenotypes, GO categories associated with the phenotype, RNAi experiments in which the phenotype was observed, genes whose knockdown resulted in the phenotype, and chains in which the phenotype participates. Biot pages are closely interlinked through biot IDs. As far as possible, biots are hyperlinked on pages. A biot page also contains hyperlinks to Wormbase and GO wherever applicable. Figure 3 illustrates the page for the gpr-1 gene through a screenshot.Figure 3.


CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining.

Pati A, Jin Y, Klage K, Helm RF, Heath LS, Ramakrishnan N - Nucleic Acids Res. (2007)

Screenshot of the gene page.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238953&req=5

Figure 3: Screenshot of the gene page.
Mentions: The web interface of CMGSDB can be used for querying. The user can search against all C. elegans biots. Genes, for example, can be searched using names, loci, transcript IDs and annotations. A biot page, apart from displaying basic information about that biot, also displays relationships with other biots that have been captured within CMGSDB. For instance, the phenotype page not only displays phenotype description, ID and source, but also shows existing relationships with other phenotypes, GO categories associated with the phenotype, RNAi experiments in which the phenotype was observed, genes whose knockdown resulted in the phenotype, and chains in which the phenotype participates. Biot pages are closely interlinked through biot IDs. As far as possible, biots are hyperlinked on pages. A biot page also contains hyperlinks to Wormbase and GO wherever applicable. Figure 3 illustrates the page for the gpr-1 gene through a screenshot.Figure 3.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.

ABSTRACT
CMGSDB (Database for Computational Modeling of Gene Silencing) is an integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains. 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. The web interface for CMGSDB is available at https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/, and serves individual biological entity information as well as details of all chains computed by CDM.

Show MeSH
Related in: MedlinePlus