Dataset Information

Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis.

ABSTRACT: Colon cancer (CC) is a heterogeneous disease influenced by complex gene networks. As such, the relationship between networks and CC should be elucidated to obtain further insights into tumour biology.Weighted gene co-expression network analysis, a powerful technique used to extract co-expressed gene networks from mRNA expressions, was conducted to identify 11 co-regulated modules in a discovery dataset with 461 patients. A transcriptional module enriched in cell cycle processes was correlated with the recurrence-free survival of the CC patients in the discovery (HR?=?0.59; 95% CI?=?0.42-0.81) and validation (HR?=?0.51; 95% CI?=?0.25-1.05) datasets. The prognostic potential of the hub gene Centromere Protein-A (CENPA) was also identified and the upregulation of this gene was associated with good survival. Another cell cycle phase-related gene module was correlated with the survival of the patients with a KRAS mutation CC subtype. The downregulation of several genes, including those found in this co-expression module, such as cyclin-dependent kinase 1 (CDK1), was associated with poor survival.Network-based approaches may facilitate the discovery of biomarkers for the prognosis of a subset of patients with stage II or III CC, these approaches may also help direct personalised therapies.

SUBMITTER: Liu R

PROVIDER: S-EPMC5424422 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis.

Liu Rong R Zhang Wei W Liu Zhao-Qian ZQ Zhou Hong-Hao HH

BMC genomics 20170509 1

<h4>Background</h4>Colon cancer (CC) is a heterogeneous disease influenced by complex gene networks. As such, the relationship between networks and CC should be elucidated to obtain further insights into tumour biology.<h4>Results</h4>Weighted gene co-expression network analysis, a powerful technique used to extract co-expressed gene networks from mRNA expressions, was conducted to identify 11 co-regulated modules in a discovery dataset with 461 patients. A transcriptional module enriched in cel ...[more]

PMID: 28486948

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Project description:Slow germination speed caused by low temperature stress intensifies the risk posed by adverse environmental factors, contributing to low germination rate and reduced production of rapeseed. The purpose of this study was to understand the transcriptional regulation mechanism for rapid germination of rapeseed. The results showed that seed components and size do not determine the seed germination speed. Different temporal transcriptomic profiles were generated under normal and low temperature conditions in genotypes with fast and slow germination speeds. Using weight gene co-expression network analysis, 37 823 genes were clustered into 15 modules with different expression patterns. There were 10 233 and 9111 differentially expressed genes found to follow persistent tendency of up- and down-regulation, respectively, which provided the conditions necessary for germination. Hub genes in the continuous up-regulation module were associated with phytohormone regulation, signal transduction, the pentose phosphate pathway, and lipolytic metabolism. Hub genes in the continuous down-regulation module were involved in ubiquitin-mediated proteolysis. Through pairwise comparisons, 1551 specific upregulated DEGs were identified for the fast germination speed genotype under low temperature stress. These DEGs were mainly enriched in RNA synthesis and degradation metabolisms, signal transduction, and defense systems. Transcription factors, including WRKY, bZIP, EFR, MYB, B3, DREB, NAC, and ERF, are associated with low temperature stress in the fast germination genotype. The aquaporin NIP5 and late embryogenesis abundant (LEA) protein genes contributed to the water uptake and transport under low temperature stress during seed germination. The ethylene/H2O2-mediated signal pathway plays an important role in cell wall loosening and embryo extension during germination. The ROS-scavenging system, including catalase, aldehyde dehydrogenase, and glutathione S-transferase, was also upregulated to alleviate ROS toxicity in the fast germinating genotype under low temperature stress. These findings should be useful for molecular assisted screening and breeding of fast germination speed genotypes for rapeseed.

Dataset Information

Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis.

Publications

Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis.

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