Data analysis Gene Expression
To enable analysis of gene expression data the Medical Biomics Centre offers training in a suite of software accessible from our hot desk computer room. These software facilitate:
- Identification of differentially expressed genes,
- Class discovery (categorizing samples into previously undescribed groups based on their gene expression profiles),
- Class prediction (classifying samples into previously defined groups based on their gene expression profiles) and
- Identification of key biological pathways and processes affected in the study/experiment.
- Quality control of microarray data,
- Normalisation using any of the popular methods, including MAS5, RMA, PLIER and LOWESS,
- Guided workflows for the identification of differentially expressed genes,
- Statistical tools and multiple test correction for assessing differential expression,
- Class discovery through Principal Component Analysis (PCA), hierarchical clustering and self-organising maps,
- Class prediction using artificial neural networks, support vector machine and decision trees and
- Biological interpretation of data through gene set enrichment analysis and pathway analysis.