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Please use this identifier to cite or link to this item: http://bura.brunel.ac.uk/handle/2438/5942

Title: GeneRank: Using search engine technology for the analysis of microarray experiments
Authors: Morrison, JL
Breitling, R
Higham, D
Gilbert, D
Keywords: GeneRank
Gene expression information
Simulated and real data
PageRank algorithm
Publication Date: 2005
Publisher: BioMed Central Ltd
Citation: BMC Bioinformatics, 6: 233, 2005
Abstract: Background: Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method – based on the PageRank algorithm employed by the popular search engine Google – that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. Results: GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion: Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.
Description: Copyright @ 2005 Morrison et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
URI: http://www.biomedcentral.com/1471-2105/6/233/abstract
http://bura.brunel.ac.uk/handle/2438/5942
DOI: http://dx.doi.org/10.1186/1471-2105-6-233
ISSN: 1471-2105
Appears in Collections:School of Information Systems, Computing and Mathematics Research Papers
Publications
Computer Science

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