Using TopoGSA from GeneCards
TopoGSA (Topology-based Gene Set Analysis), from The University of Nottingham, is a web-application dedicated to the computation and visualization of network topological properties for gene and protein sets in molecular interaction networks. TopoGSA allows you to analyze a set of genes/proteins by mapping them onto a protein interaction network and characterizing them based on multiple topological network descriptors (e.g. clustering coefficient, shortest path lengths, degrees, etc.), 2D- and 3D-visualizations and comparisons to other gene sets/pathways. Instead of uploading their own gene sets, users can also inspect pre-defined gene sets representing different metabolic pathways, functional module data bases (KEGG, BioCarta, GO, etc.) and cancer-associated gene sets and compare them against each other.
After executing a search in GeneCards, the results page provides a TopoGSA button. Clicking on it causes the set of gene symbols found by the search to be translated to Ensembl identifiers which are sent to the TopoGSA server for further analysis and visualization.
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