Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.). (13th August 2014)

• Record Type: Journal Article
• Authors: Liang, Ying-Hai; Cai, Bin; Chen, Fei; Wang, Gang; Wang, Min; Zhong, Yan; Cheng, Zong-Ming (Max)
• Is Part Of: Horticulture research. Volume 1(2014)
• Publication Date: 2014-08-13
• Subjects: Biochemical networks -- Plant molecular biology; Horticulture -- Research -- Periodicals; 635.072
• DOI: 10.1038/hortres.2014.40
• Languages: English
• ISSNs: 2052-7276

Abstract

Abstract: Gene co-expression analysis has been widely used for predicting gene functions because genes within modules of a co-expression network may be involved in similar biological processes and exhibit similar biological functions. To detect gene relationships in the grapevine genome, we constructed a grapevine gene co-expression network (GGCN) by compiling a total of 374 publically available grapevine microarray datasets. The GGCN consisted of 557 modules containing a total of 3834 nodes with 13 479 edges. The functions of the subnetwork modules were inferred by Gene ontology (GO) enrichment analysis. In 127 of the 557 modules containing two or more GO terms, 38 modules exhibited the most significantly enriched GO terms, including 'protein catabolism process', 'photosynthesis', 'cell biosynthesis process', 'biosynthesis of plant cell wall', 'stress response' and other important biological processes. The 'response to heat' GO term was highly represented in module 17, which is composed of many heat shock proteins. To further determine the potential functions of genes in module 17, we performed a Pearson correlation coefficient test, analyzed orthologous relationships with Arabidopsis genes and established gene expression correlations with real-time quantitative reverse transcriptase PCR (qRT-PCR). Our results indicated that many genes in module 17 were upregulated during the heat shock and recovery processes and downregulated in response to low temperature. Furthermore, two putative genes, Vit_07s0185g00040 and Vit_02s0025g04060, were highly expressed in response to heat shock and recovery. This study provides insight into GGCN gene modules and offers important references for gene functions and the discovery of new genes at the module level. Genetics: predicting grapevine gene function: Clustering of grapevine genes into groups based on similarities in their patterns of expression will help to reveal their biological roles. Yinghai Liang and colleagues from the Nanjing Agricultural University in China used computational analysis of 374 sets of published gene expression data to visualize 13 479 relationships between 3834 grapevine genes. The interactions between the genes in the network reveal similarities in the changes in their expression on exposure to 13 environmental stimuli and developmental changes. Genes in the same group in the network expressed at similar times and in similar places are likely to participate in similar biological processes. Many of the genes within a particular group chosen for further analysis were independently confirmed to respond to temperature extremes. Two previously uncharacterized genes in this group are now thought to mediate adaptation to heat stress.