Department of Plant Biotechnology, Dongguk Univ-Seoul, Seoul 100-715, Korea.
BMC Plant Biol. 2013 May 20;13:83. doi: 10.1186/1471-2229-13-83.
The PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org) 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.
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.
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.
植物共表达数据库（PLANEX）是一个新的基于互联网的植物基因分析数据库。PLANEX（http://planex.plantbioinformatics.org）包含来自美国国家生物技术信息中心（NCBI）基因表达综合数据库（GEO）的公开可用的 GeneChip 数据。PLANEX 是一个全基因组共表达数据库，允许从各种实验设计中对基因进行功能鉴定。它可用于鉴定基因的功能，分析基因之间的相互依赖关系。已经为其他物种开发了基因共表达数据库，但目前植物的基因共表达信息有限。
我们构建了 PLANEX，作为拟南芥、大豆、大麦、水稻、番茄、小麦、葡萄和玉米的共表达基因和功能注释列表。PLANEX 报告了皮尔逊相关系数（PCC；r 值），这些系数分布于特定微阵列平台上给定基因的感兴趣范围内，对应于特定生物体。为了支持 PCC，PLANEX 对基因本体论术语和科恩氏 Kappa 值进行了富集测试，以比较共表达数据库中所有基因的功能相似性。PLANEX 使用 k-均值方法绘制了一个共表达基因的聚类网络。为了构建 PLANEX，在超级计算中心的 IBM 超级计算机高级交互执行器（AIX）上解释了各种数据集。
PLANEX 为 8 种植物物种提供了相关性数据库、聚类网络和富集测试结果的解释。一个典型的共表达基因会生成包含数百个感兴趣基因的共表达数据列表，用于富集分析。此外，还可以使用“共表达基因比较”功能，根据比较基因组学识别和编目共表达基因。这种类型的分析将有助于解释实验数据，并确定感兴趣基因之间是否存在共同术语。
