title: EnrichNet: network-based gene set enrichment analysis.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  EnrichNet is freely available at http://www.enrichnet.org.
  
  
  BACKGROUND
  Natalio.Krasnogor@nottingham.ac.uk, reinhard.schneider@uni.lu or avalencia@cnio.es
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics Online.
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Enrico
authors.initials: E
authors.lastname: Glaab
authors.forename: Anaïs
authors.initials: A
authors.lastname: Baudot
authors.forename: Natalio
authors.initials: N
authors.lastname: Krasnogor
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schneider
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
mesh_terms: D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D005796:Genes; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism; D010300:Parkinson Disease / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D012984:Software