EnrichNet: network-based gene set enrichment analysis

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Interpretation, Statistical
  • Databases, Genetic
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Genes
  • Humans
  • Internet
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Parkinson Disease / genetics
  • Parkinson Disease / metabolism
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps
  • Software*