GIST: A Gibbs sampler to identify intracellular signal transduction pathways

Jinghua Gu, Chen Wang, Ie Ming Shih, Tian Li Wang, Yue Wang, Robert Clarke, Jianhua Xuan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Identification of intracellular signal transduction pathways plays an important role in understanding the mechanisms of how cells respond to external stimuli. The availability of high throughput microarray expression data and accumulating knowledge of protein-protein interactions have provided us with useful information to infer condition-specific signal transduction pathways. We propose a novel method called Gibbs sampler to Infer Signal Transduction pathways (GIST) to search dys-regulated pathways from large-scale protein-protein interaction networks. GIST incorporates different knowledge sources to extract paths that are highly associated with biological phenotypes or clinical information. One of the most attractive features of GIST is that the algorithm will not only provide the single optimal path according to the defined cost function but also reveal multiple suboptimal paths as alternative solutions, which can be utilized to study the pathway crosstalk. As a proof-of-concept, we test our GIST algorithm on yeast PPI networks and the identified MAPK signaling pathways are well supported by existing biological knowledge. We also apply the GIST algorithm onto a breast cancer patient dataset to show its feasibility of identifying potential pathways for further biological validation.

Original languageEnglish (US)
Title of host publication33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
Pages2434-2437
Number of pages4
DOIs
StatePublished - 2011
Externally publishedYes
Event33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011 - Boston, MA, United States
Duration: Aug 30 2011Sep 3 2011

Publication series

NameProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN (Print)1557-170X

Other

Other33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
CountryUnited States
CityBoston, MA
Period8/30/119/3/11

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  • Cite this

    Gu, J., Wang, C., Shih, I. M., Wang, T. L., Wang, Y., Clarke, R., & Xuan, J. (2011). GIST: A Gibbs sampler to identify intracellular signal transduction pathways. In 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011 (pp. 2434-2437). [6090677] (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/IEMBS.2011.6090677