title: PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.
abstract: BACKGROUND
  Over the past decade, pathway and gene-set enrichment analysis has evolved into the study of high-throughput functional genomics. Owing to poorly annotated and incomplete pathway data, researchers have begun to combine pathway and gene-set enrichment analysis as well as network module-based approaches to identify crucial relationships between different molecular mechanisms.
  
  
  METHODS
  To meet the new challenge of molecular phenotype discovery, in this work, we have developed an integrated online database, the Pathway And Gene Enrichment Database (PAGED), to enable comprehensive searches for disease-specific pathways, gene signatures, microRNA targets, and network modules by integrating gene-set-based prior knowledge as molecular patterns from multiple levels: the genome, transcriptome, post-transcriptome, and proteome.
  
  
  RESULTS
  The online database we developed, PAGED http://bio.informatics.iupui.edu/PAGED is by far the most comprehensive public compilation of gene sets. In its current release, PAGED contains a total of 25,242 gene sets, 61,413 genes, 20 organisms, and 1,275,560 records from five major categories. Beyond its size, the advantage of PAGED lies in the explorations of relationships between gene sets as gene-set association networks (GSANs). Using colorectal cancer expression data analysis as a case study, we demonstrate how to query this database resource to discover crucial pathways, gene signatures, and gene network modules specific to colorectal cancer functional genomics.
  
  
  CONCLUSIONS
  This integrated online database lays a foundation for developing tools beyond third-generation pathway analysis approaches on for discovering molecular phenotypes, especially for disease-associated pathway/gene-set enrichment analysis.
authors.affiliation: School of Informatics, Indiana University, Indianapolis, IN 46202, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Huang
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Wu
authors.forename: Madhankumar
authors.initials: M
authors.lastname: Sonachalam
authors.forename: Sammed N
authors.initials: SN
authors.lastname: Mandape
authors.forename: Ragini
authors.initials: R
authors.lastname: Pandey
authors.forename: Karl F
authors.initials: KF
authors.lastname: MacDorman
authors.forename: Ping
authors.initials: P
authors.lastname: Wan
authors.forename: Jake Y
authors.initials: JY
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D015179:Colorectal Neoplasms / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020543:Proteome; D012984:Software; D059467:Transcriptome
chemical_list: D020543:Proteome