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Mining TCGA Database for Tumor Microenvironment-Related Genes of Prognostic Value in Hepatocellular Carcinoma
- Source :
- BioMed Research International, Vol 2019 (2019), BioMed Research International
- Publication Year :
- 2019
- Publisher :
- Hindawi Limited, 2019.
-
Abstract
- Hepatocellular carcinoma (HCC) is one of the most common and lethal malignancies. Recent studies reveal that tumor microenvironment (TME) components significantly affect HCC growth and progression, particularly the infiltrating stromal and immune cells. Thus, mining of TME-related biomarkers is crucial to improve the survival of patients with HCC. Public access of The Cancer Genome Atlas (TCGA) database allows convenient performance of gene expression-based analysis of big data, which contributes to the exploration of potential association between genes and prognosis of a variety of malignancies, including HCC. The “Estimation of STromal and Immune cells in MAlignant Tumors using Expression data” algorithm renders the quantification of the stromal and immune components in TME possible by calculating the stromal and immune scores. Differentially expressed genes (DEGs) were screened by dividing the HCC cohort of TCGA database into high- and low-score groups according to stromal and immune scores. Further analyses of functional enrichment and protein-protein interaction networks show that the DEGs are mainly involved in immune response, cell adhesion, and extracellular matrix. Finally, seven DEGs have significant association with HCC poor outcomes. These genes contain FABP3, GALNT5, GPR84, ITGB6, MYEOV, PLEKHS1, and STRA6 and may be candidate biomarkers for HCC prognosis.
- Subjects :
- Male
0301 basic medicine
Carcinoma, Hepatocellular
Stromal cell
Article Subject
lcsh:Medicine
Biology
computer.software_genre
General Biochemistry, Genetics and Molecular Biology
Cohort Studies
03 medical and health sciences
0302 clinical medicine
Immune system
Text mining
Databases, Genetic
Biomarkers, Tumor
Tumor Microenvironment
Carcinoma
medicine
Humans
Protein Interaction Maps
Gene
Regulation of gene expression
Tumor microenvironment
General Immunology and Microbiology
Database
business.industry
Gene Expression Profiling
Liver Neoplasms
lcsh:R
Computational Biology
General Medicine
Middle Aged
Prognosis
medicine.disease
digestive system diseases
Gene Expression Regulation, Neoplastic
030104 developmental biology
030220 oncology & carcinogenesis
Hepatocellular carcinoma
Female
business
computer
Algorithms
Genes, Neoplasm
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 23146141 and 23146133
- Volume :
- 2019
- Database :
- OpenAIRE
- Journal :
- BioMed Research International
- Accession number :
- edsair.doi.dedup.....5d3281f03b76134ec0ff2dd9652bd26d