Gene Expression Analysis Of Breast Cancer

Introduction

• Breast Cancer Subtypes: Healthy, Basal, Her2, Luminal A, Luminal B

    subtype  n
1   Healthy 11
2     Basal 41
3      Her2 30
4 Luminal A 29
5 Luminal B 30

• We consider 26468 genes and 141 samples.

• Differential Gene Expression Analysis

  • Identify Enriched Pathways

Data

• Gene Expression Matrix

          GSM1116084 GSM1116085 GSM1116086
1007_s_at    9.47065    9.67440   10.20800
1053_at      8.36311    8.72194    7.78601
117_at       5.95426    7.02523    6.39671
1294_at      6.02119    7.24581    6.85310
1316_at      3.22997    3.29352    3.26204

• Phenotype (Sample) Metadata

               diagnosis subtype
GSM1116084 Breast cancer   Basal
GSM1116085 Breast cancer   Basal

• Feature (Gene) Metadata

        Gene.Symbol                                  Gene.Title ENTREZ_GENE_ID
1053_at        RFC2 replication factor C (activator 1) 2, 40kDa           5982

PCA Plot of Expression Data

Patterns of gene expression within one subtype differ generally from other subtypes.

Differential Expression Results

Most Significant Pathways - Basal

BP_df <- msigdbr(species = "human", category = "C5", subcategory = "BP")
pathways <- split(BP_df$gene_symbol, f = BP_df$gs_name)
fgseaRes <- fgseaMultilevel(
  pathways = pathways,
  stats    = stats,
  minSize  = 15,
  maxSize  = 500)

Leading Edge Genes in Top 5 Pathways - Basal

Network modules (Louvain detection)

Conclusion

• PCA plot

• Differential Gene Expression Analysis:

  • Basal vs Luminal A: cell division
  • Cancer vs Healthy: immune response disruption, cell division enhancement, transcription deregulation