title: EXPath: a database of comparative expression analysis inferring metabolic pathways for plants.
abstract: BACKGROUND
  In general, the expression of gene alters conditionally to catalyze a specific metabolic pathway. Microarray-based datasets have been massively produced to monitor gene expression levels in parallel with numerous experimental treatments. Although several studies facilitated the linkage of gene expression data and metabolic pathways, none of them are amassed for plants. Moreover, advanced analysis such as pathways enrichment or how genes express under different conditions is not rendered.
  
  
  METHODS
  Therefore, EXPath was developed to not only comprehensively congregate the public microarray expression data from over 1000 samples in biotic stress, abiotic stress, and hormone secretion but also allow the usage of this abundant resource for coexpression analysis and differentially expression genes (DEGs) identification, finally inferring the enriched KEGG pathways and gene ontology (GO) terms of three model plants: Arabidopsis thaliana, Oryza sativa, and Zea mays. Users can access the gene expression patterns of interest under various conditions via five main functions (Gene Search, Pathway Search, DEGs Search, Pathways/GO Enrichment, and Coexpression analysis) in EXPath, which are presented by a user-friendly interface and valuable for further research.
  
  
  CONCLUSIONS
  In conclusion, EXPath, freely available at http://expath.itps.ncku.edu.tw, is a database resource that collects and utilizes gene expression profiles derived from microarray platforms under various conditions to infer metabolic pathways for plants.
authors.forename: Chia-Hung
authors.initials: CH
authors.lastname: Chien
authors.forename: Chi-Nga
authors.initials: CN
authors.lastname: Chow
authors.forename: Nai-Yun
authors.initials: NY
authors.lastname: Wu
authors.forename: Yi-Fan
authors.initials: YF
authors.lastname: Chiang-Hsieh
authors.forename: Ping-Fu
authors.initials: PF
authors.lastname: Hou
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D063990:Gene Ontology; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000706:statistics & numerical data; D012275:Oryza / Q000235:genetics; D010944:Plants / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics