McMaster University

Centre for
Functional Genomics

Scope of Search

PCA analysis, Her2/Neu tumor, Her2/Neu tumor and BT-20 breast cancer cell line

Bioinformatics

We offer bioinformatics tools for analysis of gene expression, alternative splicing, copy number variation (CNV), loss of heterozygosity (LOH), integrative genomics, pathway interactions and gene ontology (GO) annotation. We use software compatible with the Affymetrix Gene Chip platform including Partek Genomics Suite v. 6.5, Bio Conductor and R.

We can perform:

  • Gene expression analysis/parametric and non-parametric tests/Anova/multiple testing/remove batch effect/repeated measures
  • Clustering/Principal Component Analysis (PCA)/Correlation
  • Classification and prediction
  • Survival analysis/Kaplan-Meier/Cox regression
  • Gene Set Enrichment, Gene Set Anova, GO Enrichment
  • Pathway analysis and network interactions
  • Correlate/merge CN with gene expression and LOH
  • detect allelic imbalance and find allele specific CN
  • Find genomic regions of recurrent aberrations in multiple samples
  • Alternative splicing
  • We use a number of third-party software such as Onto Express, ErmineJ, Cytoskape, Ingenuity Pathways, GSEA to gain deeper insights into gene regulatory networks and molecular function, which we have recently utilized to correlate the phenotype of murine mammary tumors to those of primary human breast cancers and elucidate the mechanism of action of novel anti-cancer agents.

To identify regions of significant copy number changes, LOH and annotate CNV we can also use the Affymetrix Genotyping console and Chromosome Analysis Suite software. Downstream statistical analyses including correlations and cluster genomes, a number of visualization options and integration with expression data can also be performed.

The Bioinformatics suite has two HP work stations with the above listed software available for advanced users at no charge. We also provide training and statistical analyses for interested parties. For more information please contact Dr. John Hassell.