/Breast-Cancer-Differential-Gene-Expression-Analysis

Differential Gene Expression (DGE) Analysis in Curated Microarray Data of Breast Cancer Subtypes

Primary LanguageR

Breast Cancer Differential Gene Expression Analysis

Differential Gene Expression (DGE) Analysis in Microarray Data of Breast Cancer Subtypes

Objectives :

  1. Perform gene filtering to filter out less expressive genes.
  2. Give recommendations for genes that are expressed differently between four cancer subtypes: Luminal A, Luminal B, Basal, and HER.
  3. Investigate genes that are expressed differently between normal cell and cancer cell.

Set

  • Dataset: GSE45827 on breast cancer gene expression from Curated Microarray Database (CuMiDa);
  • Platform: GPL 570
  • Filtering: genefilter;
  • Gene Expression Analysis: limma, t-test;
  • Gene Ontology: GO.db.

About The Data

Dataset GSE45827 on breast cancer gene expression from CuMiDa

  • 6 classes
  • 54676 genes
  • 151 samples

Algorithm included

  • Sampling
  • Gene filtering
  • Gene expression analysis: LIMMA (linear models for microarray data), t-test
  • Gene ontology