title: Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.
abstract: We have developed a web-based system (Pathway Miner) for visualizing gene expression profiles in the context of biological pathways. Pathway Miner catalogs genes based on their role in metabolic, cellular and regulatory pathways. A Fisher exact test is provided as an option to rank pathways. The genes are mapped onto pathways and gene product association networks are extracted for genes that co-occur in pathways. The networks can be filtered for analysis based on user-selected options.
  
  
  BACKGROUND
  Pathway Miner is a freely available web accessible tool at http://www.biorag.org/pathway.html
authors.affiliation: Bioinformatics Core, Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA.
authors.forename: Ritu
authors.initials: R
authors.lastname: Pandey
authors.forename: Raghavendra K
authors.initials: RK
authors.lastname: Guru
authors.forename: David W
authors.initials: DW
authors.lastname: Mount
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D020407:Internet; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009862:Online Systems; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface