Gene Network is a service provided by the UMCG Genetics department.
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planning to make the service publicly available during summer 2012.
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This gene network is based on a total of approximately 80,000 microarrays from Gene Expression Omnibus. We analyzed 54,736 human, 17,081 mouse and 6,023 rat Affymetrix arrays. Principal component analysis was done on probe correlation matrices of each of four platforms (two human platforms, one mouse and one rat platform), resulting in 777, 377, 677 and 375 robust principal components, respectively. These components are called transcriptional components as they hypothetically describe regulatory mechanisms of the corresponding transcriptomes, such as transcription factors or hormones. The components jointly explain between 79 and 90 % of the variance in the data depending on the species or platform.
Many of these components are well conserved across species and enriched for known biological phenomena. We therefore combined the results into a multi-species gene network with 20,000 unique human genes and were able to utilize the components to accurately predict functions for the genes. Predictions were made against pathways and gene sets in different biological databases such as the Gene Ontology and Reactome. Below is an illustration of the statistical method used for the prediction.