ArticleBioinformatics (Oxford, England)2012
AraPath: a knowledgebase for pathway analysis in Arabidopsis.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of gene expression signatures reveals hidden links among diverse biological processes in Arabidopsis.PloS one · 2014Pooled it
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- ShinyGO: a graphical gene-set enrichment tool for animals and plants.Bioinformatics (Oxford, England) · 2020Article
- iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data.BMC bioinformatics · 2018Article
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- Pan-phylum Comparison of Nematode Metabolic Potential.PLoS neglected tropical diseases · 2015Article
- Temporal Dynamics of Growth and Photosynthesis Suppression in Response to Jasmonate Signaling.Plant physiology · 2014Article
- PlantGSEA: a gene set enrichment analysis toolkit for plant community.Nucleic acids research · 2013Article
- Recent progress in the development of metabolome databases for plant systems biology.Frontiers in plant science · 2013Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
unlabelledStudying 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/.
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Registered trials
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