Mining TCGA Database for Genes with Prognostic Value in Breast Cancer

Abstract

The aim of the study was to use transcriptomics data to identify genes associated with advanced/aggressive breast cancer and their effect on survival outcomes. We used the publicly available The Cancer Genome Atlas (TCGA) database to obtain RNA sequence data from patients with less than five years survival (Poor Prognosis, n = 101), patients with greater than five years survival (Good Prognosis, n = 200), as well as unpaired normal tissue data (normal, n = 105). The data analyses performed included differential expression between groups and selection of subsets of genes, gene ontology, cell enrichment analysis, and survival analyses. Gene ontology results showed significantly reduced enrichment in gene sets related to tumor immune microenvironment in Poor Prognosis and cell enrichment analysis confirmed significantly reduced numbers of macrophages M1, CD8 T cells, plasma cells and dendritic cells in samples in the Poor Prognosis samples compared with Good Prognosis. A subset of 742 genes derived from differential expression analysis as well as genes coding for immune checkpoint molecules was evaluated for their effect on overall survival. In conclusion, this study may contribute to the better understanding of breast cancer transcriptomics and provide possible targets for further research and eventual therapeutic interventions.

BTLA biology in cancer: from bench discoveries to clinical potentials

“…However, variations in BTLA expression did not show any correlation with either clinicopathological characteristics or patient survival [ 90 ]. Similarly, Filippi et al analyzed transcriptomics data of 742 genes from the TCGA database and identified 6 IC genes, including BTLA, to be expressed at lower levels in BC patients, while in contrast to Fang et al, low BTLA expression was associated with poor disease prognosis [ 91 ].…”

FKBP3, a poor prognostic indicator, promotes the progression of LUAD via regulating ferroptosis and immune infiltration

“…The TCGA database covers most cancers, including lung cancer, colorectal cancer, breast cancer, etc. [12,13] At the same time, it also contains relatively comprehensive clinical information on tumor patients. [14] Clinical information generally includes data such as patient survival time, survival status, gender, and clinical stage.…”