AraPath: a knowledgebase for pathway analysis in Arabidopsis

UNLABELLED 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. AVAILABILITY http://bioinformatics.sdstate.edu/arapath/.

[1]  R. Fluhr,et al.  HORMONOMETER: A Tool for Discerning Transcript Signatures of Hormone Action in the Arabidopsis Transcriptome1[W][OA] , 2009, Plant Physiology.

[2]  Christina Backes,et al.  Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana , 2011, BMC Plant Biology.

[3]  Matthew A Hannah,et al.  A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana , 2005, PLoS genetics.

[4]  Yuguang Ban,et al.  Identification of metagenes and their Interactions through Large-scale Analysis of Arabidopsis Gene Expression Data , 2012, BMC Genomics.

[5]  Steven X. Ge,et al.  Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes , 2011, BMC Systems Biology.

[6]  S. Rhee,et al.  AraCyc: A Biochemical Pathway Database for Arabidopsis1 , 2003, Plant Physiology.

[7]  Yukihisa Shimada,et al.  AtCAST, a tool for exploring gene expression similarities among DNA microarray experiments using networks. , 2011, Plant & cell physiology.

[8]  A. Weiner,et al.  L2L: a simple tool for discovering the hidden significance in microarray expression data , 2005, Genome Biology.

[9]  Liliana Florea,et al.  List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists. , 2005, Gene.

[10]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[11]  Daniel A. Chamovitz,et al.  Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network , 2009, BMC Systems Biology.

[12]  L. Stein,et al.  Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages , 2005, Comparative and functional genomics.

[13]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[15]  Lonnie R. Welch,et al.  AGRIS: the Arabidopsis Gene Regulatory Information Server, an update , 2010, Nucleic Acids Res..