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