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PLANEX: the plant co-expression database

Won Cheol Yim1, Yongbin Yu2, Kitae Song1, Cheol Seong Jang3 and Byung-Moo Lee1*

Author affiliations

1 Department of Plant Biotechnology, Dongguk Univ-Seoul, Seoul, 100-715, Korea

2 Department of Healthcare informatics, The Catholic University of Korea, Seoul, 137-701, Korea

3 Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-701, Korea

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Citation and License

BMC Plant Biology 2013, 13:83  doi:10.1186/1471-2229-13-83

Published: 20 May 2013

Abstract

Background

The PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org webcite) contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization of genes for functional identification and analysis of a gene’s dependency among other genes. Gene co-expression databases have been developed for other species, but gene co-expression information for plants is currently limited.

Description

We constructed PLANEX as a list of co-expressed genes and functional annotations for Arabidopsis thaliana, Glycine max, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Triticum aestivum, Vitis vinifera and Zea mays. PLANEX reports Pearson’s correlation coefficients (PCCs; r-values) that distribute from a gene of interest for a given microarray platform set corresponding to a particular organism. To support PCCs, PLANEX performs an enrichment test of Gene Ontology terms and Cohen’s Kappa value to compare functional similarity for all genes in the co-expression database. PLANEX draws a cluster network with co-expressed genes, which is estimated using the k-mean method. To construct PLANEX, a variety of datasets were interpreted by the IBM supercomputer Advanced Interactive eXecutive (AIX) in a supercomputing center.

Conclusion

PLANEX provides a correlation database, a cluster network and an interpretation of enrichment test results for eight plant species. A typical co-expressed gene generates lists of co-expression data that contain hundreds of genes of interest for enrichment analysis. Also, co-expressed genes can be identified and cataloged in terms of comparative genomics by using the ‘Co-expression gene compare’ feature. This type of analysis will help interpret experimental data and determine whether there is a common term among genes of interest.

Keywords:
Co-expression; Database; Pearson’s correlation coefficients; Clustering