POEAS: Automated Plant Phenomic Analysis Using Plant Ontology

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 co...

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Main Authors:	Shameer, Khader, Naika, Mahantesha BN, Mathew, Oommen K, Sowdhamini, Ramanathan
Format:	Online
Language:	English
Published:	Libertas Academica 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274039/

id	pubmed-4274039
recordtype	oai_dc
spelling	pubmed-42740392015-01-08 POEAS: Automated Plant Phenomic Analysis Using Plant Ontology Shameer, Khader Naika, Mahantesha BN Mathew, Oommen K Sowdhamini, Ramanathan Original Research 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. Libertas Academica 2014-12-21 /pmc/articles/PMC4274039/ /pubmed/25574136 http://dx.doi.org/10.4137/BBI.S19057 Text en © 2014 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Shameer, Khader Naika, Mahantesha BN Mathew, Oommen K Sowdhamini, Ramanathan
spellingShingle	Shameer, Khader Naika, Mahantesha BN Mathew, Oommen K Sowdhamini, Ramanathan POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
author_facet	Shameer, Khader Naika, Mahantesha BN Mathew, Oommen K Sowdhamini, Ramanathan
author_sort	Shameer, Khader
title	POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
title_short	POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
title_full	POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
title_fullStr	POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
title_full_unstemmed	POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
title_sort	poeas: automated plant phenomic analysis using plant ontology
description	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.
publisher	Libertas Academica
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274039/
_version_	1613169835345182720

POEAS: Automated Plant Phenomic Analysis Using Plant Ontology

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