title: POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.
abstract: Biological enrichment analysis using gene ontology (GO) provides a global overview of the functional role of genes or proteins identified from large-scale genomic or proteomic experiments. Phenomic enrichment analysis of gene lists can provide an important layer of information as well as cellular components, molecular functions, and biological processes associated with gene lists. Plant phenomic enrichment analysis will be useful for performing new experiments to better understand plant systems and for the interpretation of gene or proteins identified from high-throughput experiments. Plant ontology (PO) is a compendium of terms to define the diverse phenotypic characteristics of plant species, including plant anatomy, morphology, and development stages. Adoption of this highly useful ontology is limited, when compared to GO, because of the lack of user-friendly tools that enable the use of PO for statistical enrichment analysis. To address this challenge, we introduce Plant Ontology Enrichment Analysis Server (POEAS) in the public domain. POEAS uses a simple list of genes as input data and performs enrichment analysis using Ontologizer 2.0 to provide results in two levels, enrichment results and visualization utilities, to generate ontological graphs that are of publication quality. POEAS also offers interactive options to identify user-defined background population sets, various multiple-testing correction methods, different enrichment calculation methods, and resampling tests to improve statistical significance. The availability of such a tool to perform phenomic enrichment analyses using plant genes as a complementary resource will permit the adoption of PO-based phenomic analysis as part of analytical workflows. POEAS can be accessed using the URL http://caps.ncbs.res.in/poeas.
authors.affiliation: National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.
authors.forename: Khader
authors.initials: K
authors.lastname: Shameer
authors.affiliation: National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India. ; Department of Plant Biotechnology, University of Agricultural Sciences, GKVK Campus, Bangalore, India.
authors.forename: Mahantesha Bn
authors.initials: MB
authors.lastname: Naika
authors.affiliation: National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.
authors.forename: Oommen K
authors.initials: OK
authors.lastname: Mathew
authors.affiliation: National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
keywords: Arabidopsis thaliana; phenomics; phenotype enrichment; plant genomics; plant ontology