TopoGSA

TopoGSA (Topology-based Gene Set Analysis) computes and visualise the topological properties of a set of genes/proteins mapped onto a molecular interaction network. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, are computed and compared against those of known cellular pathways and processes (KEGG, BioCarta, GO, etc.).

TopoGSA is updated twice per year to integrate newly available protein interaction data and reference gene sets. Alternatively, a user-defined networks can be uploaded and analysed. The pathways and processes similar to the uploaded set can be identified based on the 2D and 3D interactive visualisations or using an aggregated similarity measure that combines the topological properties into a single score.

Publications

• DOI eprint BibTeX
  E. Glaab, A. Baudot, N. Krasnogor, A. Valencia
  TopoGSA: network topological gene set analysis
  in Bioinformatics, 26(9):1271-1272, May 2010

  @ARTICLE{Glaab2010a,
    title = {TopoGSA: network topological gene set analysis},
    author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Valencia, A.},
    year = 2010,
    doi = {10.1093/bioinformatics/btq131},
    month = may,
    journal = {Bioinformatics},
    volume = {26},
    number = {9},
    pages = {1271--1272}
  }