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.

 

Software available in the Centre include BeadStudio (Illumina), GeneSpring (Agilent Technologies) and Ariadne Pathway Studio (Ariadne Genomics).  Functionality found within the software include:

• 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.