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Wormnet: a crystal ball for Caenorhabditis elegans.

Von Stetina SE, Mango SE - Genome Biol. (2008)

Bottom Line: An integrated gene network for Caenorhabditis elegans using data from multiple genome-wide screens encompasses most protein-coding genes and can accurately predict their phenotypes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Huntsman Cancer Institute, University of Utah, Circle of Hope, Salt Lake City, Utah 84112, USA. stephen.vonstetina@hci.utah.edu

ABSTRACT
An integrated gene network for Caenorhabditis elegans using data from multiple genome-wide screens encompasses most protein-coding genes and can accurately predict their phenotypes.

Show MeSH
The conceptual framework of Wormnet. Wormnet was generated from large-scale studies of C. elegans biology (boxes). Data for each gene were weighted according to their accuracy, which is diagrammed here as differently sized boxes. Wormnet can be used to make predictions about gene function, which can be rapidly tested in vivo. 'Associalogs' refers to physical or genetic interaction data from yeast, flies, and humans mapped to their nematode orthologs.
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Figure 1: The conceptual framework of Wormnet. Wormnet was generated from large-scale studies of C. elegans biology (boxes). Data for each gene were weighted according to their accuracy, which is diagrammed here as differently sized boxes. Wormnet can be used to make predictions about gene function, which can be rapidly tested in vivo. 'Associalogs' refers to physical or genetic interaction data from yeast, flies, and humans mapped to their nematode orthologs.

Mentions: Now, Lee and colleagues [1] have assembled diverse data from C. elegans large-scale analyses to build a probabilistic network, dubbed Wormnet. Much of the information used by Zhong and Sternberg was also used by Lee et al. Additional information in Wormnet was derived from the following sources: gene interactions inferred from co-citation analysis, with the assumption that gene pairs that are co-cited in abstracts more than the random expectation are likely to be functionally linked; 'associalogs', which represent physical or genetic interaction data from other species mapped onto their C. elegans orthologs, as determined by INPARANOID [11,12]; and phylogenetic and gene neighbor analysis using 117 bacterial genomes (Figure 1). The current study excluded Gene Ontology (GO) terms and RNAi phenotypic data, opting to use this information for data weighting and validation, respectively.


Wormnet: a crystal ball for Caenorhabditis elegans.

Von Stetina SE, Mango SE - Genome Biol. (2008)

The conceptual framework of Wormnet. Wormnet was generated from large-scale studies of C. elegans biology (boxes). Data for each gene were weighted according to their accuracy, which is diagrammed here as differently sized boxes. Wormnet can be used to make predictions about gene function, which can be rapidly tested in vivo. 'Associalogs' refers to physical or genetic interaction data from yeast, flies, and humans mapped to their nematode orthologs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2481412&req=5

Figure 1: The conceptual framework of Wormnet. Wormnet was generated from large-scale studies of C. elegans biology (boxes). Data for each gene were weighted according to their accuracy, which is diagrammed here as differently sized boxes. Wormnet can be used to make predictions about gene function, which can be rapidly tested in vivo. 'Associalogs' refers to physical or genetic interaction data from yeast, flies, and humans mapped to their nematode orthologs.
Mentions: Now, Lee and colleagues [1] have assembled diverse data from C. elegans large-scale analyses to build a probabilistic network, dubbed Wormnet. Much of the information used by Zhong and Sternberg was also used by Lee et al. Additional information in Wormnet was derived from the following sources: gene interactions inferred from co-citation analysis, with the assumption that gene pairs that are co-cited in abstracts more than the random expectation are likely to be functionally linked; 'associalogs', which represent physical or genetic interaction data from other species mapped onto their C. elegans orthologs, as determined by INPARANOID [11,12]; and phylogenetic and gene neighbor analysis using 117 bacterial genomes (Figure 1). The current study excluded Gene Ontology (GO) terms and RNAi phenotypic data, opting to use this information for data weighting and validation, respectively.

Bottom Line: An integrated gene network for Caenorhabditis elegans using data from multiple genome-wide screens encompasses most protein-coding genes and can accurately predict their phenotypes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Huntsman Cancer Institute, University of Utah, Circle of Hope, Salt Lake City, Utah 84112, USA. stephen.vonstetina@hci.utah.edu

ABSTRACT
An integrated gene network for Caenorhabditis elegans using data from multiple genome-wide screens encompasses most protein-coding genes and can accurately predict their phenotypes.

Show MeSH