title: AraPath: a knowledgebase for pathway analysis in Arabidopsis.
abstract: Studying plants using high-throughput genomics technologies is becoming routine, but interpretation of genome-wide expression data in terms of biological pathways remains a challenge, partly due to the lack of pathway databases. To create a knowledgebase for plant pathway analysis, we collected 1683 lists of differentially expressed genes from 397 gene-expression studies, which constitute a molecular signature database of various genetic and environmental perturbations of Arabidopsis. In addition, we extracted 1909 gene sets from various sources such as Gene Ontology, KEGG, AraCyc, Plant Ontology, predicted target genes of microRNAs and transcription factors, and computational gene clusters defined by meta-analysis. With this knowledgebase, we applied Gene Set Enrichment Analysis to an expression profile of cold acclimation and identified expected functional categories and pathways. Our results suggest that the AraPath database can be used to generate specific, testable hypotheses regarding plant molecular pathways from gene expression data.
  
  
  BACKGROUND
  http://bioinformatics.sdstate.edu/arapath/.
authors: Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA.
authors: Liming
authors: L
authors: Lai
authors: Arthur
authors: A
authors: Liberzon
authors: Jason
authors: J
authors: Hennessey
authors: Gaixin
authors: G
authors: Jiang
authors: Jianli
authors: J
authors: Qi
authors: Jill P
authors: JP
authors: Mesirov
authors: Steven X
authors: SX
authors: Ge
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D051188:Knowledge Bases; D005810:Multigene Family