This talk is based on joint work with Kord Eickmeyer, Lior Pachter, and Ruriko Yoshida.
Following an idea of Ideker et al. (2002), we introduced the GXNA algorithm, which uses a gene interaction network to search for differentially expressed groups of related genes. GXNA has several desirable features, such as fast runtimes and the computation of significance levels adjusted for multiple testing. We give an overview of the algorithm and compare it with some of the alternatives. On several data sets related to the immunology of cancer, GXNA identifies interesting pathways that are not found by single-gene analysis.
We also give a brief overview of the publicly available software that implements the algorithm, and of ongoing work to improve its performance and user interface.
This is joint work with Susan Holmes, Rebecca Critchley-Thorne, and Peter Lee.
R. Critchley-Thorne, N. Yan, Ş. Nacu, S. Holmes, and P. P. Lee. Inhibition of interferon signaling in lymphocytes in metastatic melanoma patients. PLoS Medicine (2007).
T. Ideker, O. Ozier, B. Schwikowski, and A. Siegel. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (2002).
Ş. Nacu, R. Critchley-Thorne, P. P. Lee, and S. Holmes. Gene expression network analysis, and applications to immunology. Bioinformatics (2007).
1. Biology- molecular biology techniques, genomics, proteomics, and metabolomics.
2. Chemistry- chemical structure identification, analytical chemistry, pharmacology and process chemistry.
3. Clinical trials- how do you answer a clinical question?
I shall present in my talk
(1) A system to catalogue disease-alleles onto the human genome sequence.
(2) A comprehensive and current "human disease gene" collection, consisting of over 2,200 genes with documented associations predisposing to diverse disease phenotypes.
(3) Implications and challenges for medical applications.