Sialyl-Tn in triple negative breast cancer: gaining insights into a novel subgroup.

Autors: Rita Adubeiro Lourenço, Daniela Barreira, Carla Lopes, Pedro Granjo, Ana Sofia Rodrigues, Zélia Silva, Manuela Martins, Ana Rita Grosso, Paula A Videira

Table of Contents

• Project Aim
• Requirements
• Performed Analysis

Project Aim

The study aimed to elucidate the expression, clinical implications, and biological context of the sialyl-Tn (STn) antigen in Triple Negative Breast Cancer (TNBC). With that in mind, two types of cohorts and datasets were used in this analysis. The first one, named HSJ-TNBC, comprises a dataset of tumour tissue microarray staining data and clinical information and the second one, named TCGA-TNBC, is a dataset retrieved from The Cancer Genome Atlas (TCGA) database and includes transcriptomic and clinical data.

Requirements

To run the scripts it is required R (programming language) with the following packages installed:

• survival
• survminer
• readxl
• tidyverse
• openxlsx
• corrplot
• BiocManager
• TCGAbiolinks
• SummarizedExperiment
• futile.logger
• EnsDb.Hsapiens.v86
• biomaRt
• limma
• ggrepel

Performed Analysis for the paper

• Overall and progression-free survival analysis
• Contingency tables analysis
• Correlation analysis
• Comparison analysis
• Retrieving data from the TCGA database
• Selecting a subgroup of tumours (TNBC)
• Differential Expression Analysis