A method for finding communities of related genes

We present a method for creating a network of gene co-occurrences from the literature and partitioning it into communities of related genes. The way in which our method identifies communities makes it likely that the component genes of each community will be related by their function. The method pro...

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Veröffentlicht in:Proceedings of the National Academy of Sciences - PNAS 2004-04, Vol.101 (Suppl 1), p.5241-5248
Hauptverfasser: Wilkinson, Dennis M, Huberman, Bernardo A
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container_title Proceedings of the National Academy of Sciences - PNAS
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creator Wilkinson, Dennis M
Huberman, Bernardo A
description We present a method for creating a network of gene co-occurrences from the literature and partitioning it into communities of related genes. The way in which our method identifies communities makes it likely that the component genes of each community will be related by their function. The method processes a large database of article abstracts, synthesizing information from many sources to shed light on groups of genes that have been shown to interact. It is a tool to be used by researchers in the biomedical sciences to swiftly search for known interactions and to provide insight into unexplored connections. The partitioning procedure is designed to be particularly applicable to large networks in which individual nodes may play a role in more than one community. In this paper, we explain the details of the method, in particular the partitioning process. We also apply the method to produce communities of genes related to colon cancer and show that the results are useful.
doi_str_mv 10.1073/pnas.0307740100
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subjects Colonic Neoplasms - genetics
Databases, Factual
Genes
Genes - genetics
Humans
MEDLINE
Methods
Neoplasms - genetics
Neural Networks, Computer
Proteins - genetics
RNA - genetics
United States
title A method for finding communities of related genes
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