Gene Coexpression Analysis

Gene expression data from fifteen different rice gene expression experiments have been analyzed to identify modules of genes with highly correlated expression patterns. Gene coexpression modules were identified using the WGCNA method (Zhang et al 2005). In this analysis, the data from the individual experiments were analyzed separately. The total number of genes analzyed in each experiment was reduced to remove unexpressed genes, constitutive genes and genes with slight expression variation using a coefficient of variation filter. The gene report pages for genes that were included in these analyses have a Gene Associations section that shows a trend plot of the normalized gene expression values for each gene from a single module.

Details about each experiment and the gene modules identified within each can be found on the experiment report pages:

Arsenate response in roots by cultivars Azucena and Bala (GSE4471)
Cytokinin response in roots and leaves (GSE6719)
Inflorescence and seed developmental series (GSE6893)
Abiotic stress treatment of rice seedlings (GSE6901)
Striga hermonthica infection time course for IAC165 and Nipponbare (GSE10373)
Rice stripe virus infection of cultivars WuYun3 and KT95 (GSE11025)
Analysis of gibberellin-signaling mutants (GSE15046)
Infection by Xanthomonas oryzae pv. oryzae or by X. oryzae pv. oryzicola (GSE16793)
Iron and phosphorus interaction in rice seedlings (GSE17245)
Root infection time course with Magnaporthe oryzae strain Guy11 (GSE18361)
Tissue atlas from Minghui 63 rice (GSE19024)
Infection with Xanthomonas oryzae pv. oryzicola of rice carrying maize-Rxo1 (GSE19239)
Rice aerobic germination time course (E-MEXP-1766)
Rice anaerobic/aerobic germination time course (E-MEXP-2267)
Rice leaf and stem tissues thermoperiod/photoperiod time courses (E-MEXP-2506)

Four search tools have been developed to help researchers explore these gene coexpression results.

The gene coexpression analyses were performed with release 6.1 gene models. See the FAQ page for more information.

Files related to these analyses can be found on our ftp site.

A manuscript describing these analyses is available: Childs KL, Davidson RM, Buell CR (2011) Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes. PLoS ONE 6(7): e22196


NSF Logo This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation.