Gene Set Enrichment Analysis is one of many approaches to the analysis of gene expression profile data and is described in a paper from workers at the Broad Institute. The basic concept was prompted by the observation that studying individual genes showing the most significant difference in expression level between two states or phenotypes is lacking [...]
Author Archives: Paul Denny
Pathway Analysis using the Gene Set Enrichment Analysis (GSEA) Tool
Posted in Pathway analysis
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Joys of editing academic science books
Or: “A beginner’s guide to herding cats”. Consider this scenario: you are an academic scientist, in a busy research institute and your boss is invited to edit a book, but declines due to pressure of work; then suggests that it would look good on your CV. You agree, it would look good on your CV, so [...]
Posted in Light relief
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How does a mutation in a transcription factor cause glue ear?
Acute otitis media, sometimes known as “glue ear”, is the most common bacterial infection in children and by 1 year of age about 60% of children will have had one episode. In some cases, children develop a chronic condition, which, despite the infection being cured, the “glue” doesn’t go away and causes deafness. In an [...]
Posted in Pathway analysis, Target discovery
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Target discovery in childhood-onset asthma
Asthma is caused by a combination of environmental and genetic influences, but the specific factors are poorly understood. A significant “hit” detected in a genome-wide association scan (GWAS) for childhood asthma led a client to believe that one gene might be partially responsible. Proving that this genetic association really was causing asthma was, however, difficult. Firstly, [...]
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Pathway analysis of gene expression data – male reduced fertility / sterility
A group of animals that can breed and produce fertile offspring is one of the definitions of a species. This means that the biological mechanisms of fertility and infertility are of interest not only to evolutionary biologists, but also to clinicians and of course to the wider public. At the Institute of Molecular Genetics in [...]
Posted in Pathway analysis, Target discovery
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Target discovery in inherited muscle weakness
Muscle weakness can be caused by a rare inherited disease called myofibrillar myopathy. Gonzalo Blanco’s team found a mouse model of this disease and wanted to identify the underlying cause of the severe muscle weakness. Their aim was to discover potential therapeutic targets to translate into pre-clinical and clinical studies. Before I became involved, the disease had [...]
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