Screening TCGA database for prognostic genes in lower grade glioma microenvironment.

ABSTRACT:

Background

To identify prognostic hub genes which associated with tumor microenvironment (TME) in lower grade glioma (LGG) of central nervous system.

Methods

We downloaded LGG patients gene transcriptome profiles of the central nervous system in The Cancer Genome Atlas (TCGA) database. Clinical characteristics and survival data through the Genomic Data Commons (GDC) tool were extracted. We used limma package for normalization processing. Scores of immune, stromal and ESTIMATE were calculated using ESTIMATE algorithm. Then, box plots were applied to explore the association between immune scores, stromal scores, ESTIMATE scores and histological type, tumor grade. Kaplan-Meier (K-M) analysis was utilized to explore the prognostic value of scores. Furthermore, heatmaps and volca

SUBMITTER: Ni J 

PROVIDER: S-EPMC7154476 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature