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LPIA is a computational method for identifying biological pathways as putative sources of transcriptional dysregulation. It looks for statistically signficant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell.

Details about the method may be found in

Pham, L., Christadore, L., Schaus, S., and Kolaczyk, E.D. (2011). Network-based prediction for sources of transcriptional dysregulation via latent pathway identification analysis. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1100891108.

Materials necessary for running LPIA may be found here. These include

  • Code for running LPIA .
  • KEGG and Gene Ontology gene sets used in the LPIA paper, curated for use with LPIA.


Questions about using the LPIA software? Please contact Lisa Pham .