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 publicationProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
Pages2434-2437
Number of pages4
DOIs
StatePublished - 2011
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

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

Fingerprint

Signal transduction
Signal Transduction
Proteins
Protein Interaction Maps
Microarrays
Crosstalk
Yeasts
Cost functions
Yeast
Breast Neoplasms
Phenotype
Costs and Cost Analysis
Throughput
Availability

ASJC Scopus subject areas

  • Computer Vision and Pattern Recognition
  • Signal Processing
  • Biomedical Engineering
  • Health Informatics

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 Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS (pp. 2434-2437). [6090677] https://doi.org/10.1109/IEMBS.2011.6090677

GIST : A Gibbs sampler to identify intracellular signal transduction pathways. / Gu, Jinghua; Wang, Chen; Shih, Ie Ming; Wang, Tian-Li; Wang, Yue; Clarke, Robert; Xuan, Jianhua.

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. 2011. p. 2434-2437 6090677.

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

Gu, J, Wang, C, Shih, IM, Wang, T-L, Wang, Y, Clarke, R & Xuan, J 2011, GIST: A Gibbs sampler to identify intracellular signal transduction pathways. in Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS., 6090677, pp. 2434-2437, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011, Boston, MA, United States, 8/30/11. https://doi.org/10.1109/IEMBS.2011.6090677
Gu J, Wang C, Shih IM, Wang T-L, Wang Y, Clarke R et al. GIST: A Gibbs sampler to identify intracellular signal transduction pathways. In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. 2011. p. 2434-2437. 6090677 https://doi.org/10.1109/IEMBS.2011.6090677
Gu, Jinghua ; Wang, Chen ; Shih, Ie Ming ; Wang, Tian-Li ; Wang, Yue ; Clarke, Robert ; Xuan, Jianhua. / GIST : A Gibbs sampler to identify intracellular signal transduction pathways. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. 2011. pp. 2434-2437
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