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Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.

EnrichNet: network-based gene set enrichment analysis.

Author information

1
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg.

Abstract

MOTIVATION:

Assessing functional associations between an experimentally derived gene or protein set of interest and a database of known gene/protein sets is a common task in the analysis of large-scale functional genomics data. For this purpose, a frequently used approach is to apply an over-representation-based enrichment analysis. However, this approach has four drawbacks: (i) it can only score functional associations of overlapping gene/proteins sets; (ii) it disregards genes with missing annotations; (iii) it does not take into account the network structure of physical interactions between the gene/protein sets of interest and (iv) tissue-specific gene/protein set associations cannot be recognized.

RESULTS:

To address these limitations, we introduce an integrative analysis approach and web-application called EnrichNet. It combines a novel graph-based statistic with an interactive sub-network visualization to accomplish two complementary goals: improving the prioritization of putative functional gene/protein set associations by exploiting information from molecular interaction networks and tissue-specific gene expression data and enabling a direct biological interpretation of the results. By using the approach to analyse sets of genes with known involvement in human diseases, new pathway associations are identified, reflecting a dense sub-network of interactions between their corresponding proteins.

AVAILABILITY:

EnrichNet is freely available at http://www.enrichnet.org.

CONTACT:

Natalio.Krasnogor@nottingham.ac.uk, reinhard.schneider@uni.lu or avalencia@cnio.es

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics Online.

PMID:
22962466
PMCID:
PMC3436816
DOI:
10.1093/bioinformatics/bts389
[Indexed for MEDLINE]
Free PMC Article

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