POEAS - Plant Ontology Enrichment Analysis Server:
Phenomic analysis of gene lists can provide an important layer of information for performing new experiments to understand plant systems. Systematic interpretation of gene or proteins identified from high-throughput experiments using phenotype annotations help to understand the phenomic a
ssociations. Plant Ontology (PO) offers an ontological framework for describing plant phenomic charecterestics including plant anatomy, morphology and plant development stages. Adoption of this highly useful ontology was limited due to unavailability of tools to use the ontology for statistical enrichment analysis. To address this problem, we introduce POEAS: a plant ontology enrichment analysis server in the public domain. The server uses a simple list of genes as an input and perform enrichment analysis and provide results in two levels: a table with enrichment results and a visulaization utilitity to generate ontological graphs that can be used in publications. We envisage that Availability of such a tool as a complementary resource will enable both plant biologists and computational biologist to adopt plant ontology based phenomic analysis as part of analytical workflows.
POEAS - Methodology:
POEAS uses a simple list of genes/proteins as input and perform enrichment analysis and provide results and tools for visualizing enrichment results. Users can also plot various statistics by grouping results by genes and PO terms. The interface is developed using HTML, CSS and JavaScript. PO annotations and association data are synced to POEAS to provide uptodate results to the users. Enrichment analysis was performed using Ontologizer 2.0, a biomedical ontology enrichment analysis tool, multiple options are availble to select enrichment method and statistical approach.
Ontology Data Version: 20-08-2013
If you use POEAS data, please cite as:
Khader Shameer, Mahantesha BN Naika, Oommen K. Mathew, and Ramanathan Sowdhamini.(2014) POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. Bioinformatics and Biology Insights 2014:8 209-214
10.4137/BBI.S19057. [PMID:
25574136]
POEAS - References:
- The Plant Ontology Consortium (2002) The Plant Ontology Consortium and plant ontologies. Comp Funct Genomics, 3, 137-142.
- Bauer, S., Grossmann, S., Vingron, M. and Robinson, P.N. (2008) Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics, 24, 1650-1651.
- Avraham, S., Tung, C.W., Ilic, K., Jaiswal, P., Kellogg, E.A., McCouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M. et al. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res, 36, D449-454.
- Cooper, L., Walls, R.L., Elser, J., Gandolfo, M.A., Stevenson, D.W., Smith, B., Preece, J., Athreya, B., Mungall, C.J., Rensing, S. et al. (2012) The Plant Ontology As A Tool For Comparative Plant Anatomy And Genomic Analyses. Plant & cell physiology.
- Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E.A., McCouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M. et al. (2005) Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics, 6, 388-397.
POEAS - Team :
Prof. Ramanthan Sowdhamini (Contact : mini@ncbs.res.in)
Khader Shameer
Oommen K. Mathew
Mahantesha Naika
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