Database Mining of Genes of Prognostic Value for the Prostate Adenocarcinoma Microenvironment Using the Cancer Gene Atlas.

BioMed Research International
Xin ZhaoHonglin Cheng

Abstract

Prostate adenocarcinoma (PRAD) is a common malignant tumor in elderly men. Our research uses The Cancer Gene Atlas (TCGA) database to find potential related genes for predicting the prognosis of patients with PRAD. We downloaded gene expression profiles and clinical sample information from TCGA for 490 patients with PRAD (patient age: 41-78 years). We calculated stromal and immune scores using the ESTIMATE algorithm to predict the level of stromal and immune cell infiltration. We categorized patients with PRAD in TCGA into high and low score arrays according to their median immune/stromal scores and identified differentially expressed genes (DEGs) that were significantly correlated with the prognosis of PRAD. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. The association between DEGs and overall survival was investigated by weighted Kaplan-Meier survival analysis and multivariate analysis. Furthermore, the protein-protein interaction network (PPI) of DEGs was constructed using the STRING tool. Finally, the hub genes were identified by analyzing the degree of association of PPI networks. We found that 8 individual DEGs, C6, S100A12, MLC1, PAX5, C7, FAM162B, CAMK1G, an...Continue Reading

References

Jan 27, 2000·Cell·D Hanahan, R A Weinberg
May 23, 2003·Journal of Cellular Biochemistry·Yan-Xi SunRussell S Taichman
Feb 21, 2004·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·David J Grignon
Mar 4, 2008·Cellular & Molecular Biology Letters·Pooi-Fong Wong, Sazaly Abubakar
Jun 12, 2008·Frontiers of Radiation Therapy and Oncology·M SiaP Warde
Jan 10, 2009·Nature Clinical Practice. Urology·Caroline M MooreMark Emberton
Sep 17, 2010·Genes & Development·Michael M Shen, Cory Abate-Shen
Nov 26, 2010·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Roy M BremnesLill-Tove Busund
Oct 12, 2013·Nature Communications·Kosuke YoshiharaRoel G W Verhaak
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 7, 2015·Acta Neuropathologica·Kenneth AldapeAndreas von Deimling
Apr 7, 2016·Japanese Journal of Clinical Oncology·Cheng PangGang Zhu
Aug 16, 2016·Breast Cancer Research : BCR·Karen M BussardFrank C Marini
Dec 8, 2016·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Aug 10, 2017·Oncology Letters·Binbin YinZhihua Tao
Nov 21, 2017·Cancer Letters·Sanjay KumarManoj Mishra
Jan 14, 2018·Gynecologic Oncology·Ghassan M SaedIra Memaj
Jun 27, 2018·International Journal of Molecular Sciences·Mengyao LiuYan Zhang
Aug 1, 2018·Molecular Cancer·Bo RenYupei Zhao
Sep 16, 2018·Phytomedicine : International Journal of Phytotherapy and Phytopharmacology·Sook-Kyoung HeoJae-Cheol Jo
Jan 1, 2019·Hypertension·Kaoru KawasakiIkuo Konishi
Jun 12, 2019·The Journal of Steroid Biochemistry and Molecular Biology·Yin-Gi JangKyung-Chul Choi

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Software Mentioned

STRING
limma
R
TCGA
R package of survey
R Project for Statistical Computing
ESTIMATE

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