Bioinformatics Analysis to Screen the Key Prognostic Genes in Tumor Microenvironment of Bladder Cancer

BioMed Research International
Zhao ZhangZhonghua Xu

Abstract

Bladder cancer (BLCA) is the fifth most common cancer and has the features of low survival rate and high morbidity and mortality. The Cancer Genome Atlas (TCGA) is a pool of global gene expression profile and contains huge amounts of cancer genomics data, which makes it possible to inquire the relationship between gene expression and prognosis of a series of malignant tumors including BLCA. Immune and stromal cells are two major components of tumor microenvironment (TME) which play an important role in judging the prognosis of tumor and influencing the progression of malignant, inflammatory, and metabolic disorders. In our study, we conducted a quantitative analysis of immune and stromal elements based on the ESTIMATE algorithm and thus divided BLCA cases into high and low groups. Then the differentially expressed genes closely related to tumor prognosis between groups were identified and had been shown to correlate with immune response and stromal alterations, which was further confirmed by functional enrichment analysis and protein-protein interaction networks. We validated those genes through BLCA dates downloaded from ArrayExpress and thus got the marker genes to predict prognosis of BLCA. Additionally, immune cell infiltra...Continue Reading

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Datasets Mentioned

BETA
E-GEOD-13507

Software Mentioned

ArrayExpress
R
clusterProfiler
title
ggplot2
ESTIMATE
Cytoscape
pheatmap
R package

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