Dataset Information

Identification of two novel biomarkers of rectal carcinoma progression and prognosis via co-expression network analysis.

ABSTRACT: mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples. A total of 16 co-expressed gene modules were identified. The green-yellow and salmon modules were most appropriate to the pathological stage (R = 0.36) and the overall survival (HR =13.534, P = 0.014), respectively. A diagnostic model of the five pathological stage hub genes (SCG3, SYP, CDK5R2, AP3B2, and RUNDC3A) provided a powerful classification accuracy between localized RC and non-localized RC. We also found increased Secretogranin III (SCG3) expression with higher pathological stage and poorer prognosis in the test and validation set. The increased Homer scaffolding protein 2 (HOMER2) expression with the favorable survival prediction efficiency significantly correlated with the markedly reduced overall survival of RC patients and the higher pathological stage during the test and validation set. Our findings indicate that the SCG3 and HOMER2 mRNA levels should be further evaluated as predictors of pathological stage and survival in patients with RC.

SUBMITTER: Sun M

PROVIDER: S-EPMC5642502 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Identification of two novel biomarkers of rectal carcinoma progression and prognosis via co-expression network analysis.

Sun Min M Sun Taojiao T He Zhongshi Z Xiong Bin B

Oncotarget 20170627 41

mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied we ...[more]

PMID: 29050227

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Project description:BackgroundGlioblastoma (GBM) is the most common malignant tumor in the central system with a poor prognosis. Due to the complexity of its molecular mechanism, the recurrence rate and mortality rate of GBM patients are still high. Therefore, there is an urgent need to screen GBM biomarkers to prove the therapeutic effect and improve the prognosis.ResultsWe extracted data from GBM patients from the Gene Expression Integration Database (GEO), analyzed differentially expressed genes in GEO and identified key modules by weighted gene co-expression network analysis (WGCNA). GSE145128 data was obtained from the GEO database, and the darkturquoise module was determined to be the most relevant to the GBM prognosis by WGCNA (r = - 0.62, p = 0.01). We performed enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal the interaction activity in the selected modules. Then Kaplan-Meier survival curve analysis was used to extract genes closely related to GBM prognosis. We used Kaplan-Meier survival curves to analyze the 139 genes in the darkturquoise module, identified four genes (DARS/GDI2/P4HA2/TRUB1) associated with prognostic GBM. Low expression of DARS/GDI2/TRUB1 and high expression of P4HA2 had a poor prognosis. Finally, we used tumor genome map (TCGA) data, verified the characteristics of hub genes through Co-expression analysis, Drug sensitivity analysis, TIMER database analysis and GSVA analysis. We downloaded the data of GBM from the TCGA database, the results of co-expression analysis showed that DARS/GDI2/P4HA2/TRUB1 could regulate the development of GBM by affecting genes such as CDC73/CDC123/B4GALT1/CUL2. Drug sensitivity analysis showed that genes are involved in many classic Cancer-related pathways including TSC/mTOR, RAS/MAPK.TIMER database analysis showed DARS expression is positively correlated with tumor purity (cor = 0.125, p = 1.07e-02)), P4HA2 expression is negatively correlated with tumor purity (cor =-0.279, p = 6.06e-09). Finally, GSVA analysis found that DARS/GDI2/P4HA2/TRUB1 gene sets are closely related to the occurrence of cancer.ConclusionWe used two public databases to identify four valuable biomarkers for GBM prognosis, namely DARS/GDI2/P4HA2/TRUB1, which have potential clinical application value and can be used as prognostic markers for GBM.

Dataset Information

Identification of two novel biomarkers of rectal carcinoma progression and prognosis via co-expression network analysis.

Publications

Identification of two novel biomarkers of rectal carcinoma progression and prognosis via co-expression network analysis.

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