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Issue No. 02 - March/April (2012 vol. 9)
ISSN: 1545-5963
pp: 438-450
L. Acharya , Dept. of Comput. Sci., Univ. of New Orleans, New Orleans, LA, USA
T. Judeh , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
Zhansheng Duan , Dept. of Comput. Sci., Univ. of New Orleans, New Orleans, LA, USA
M. Rabbat , Dept. of Electr. & Comput. Eng., McGill Univ., Montreal, QC, Canada
Dongxiao Zhu , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
Reconstruction of signaling pathway structures is essential to decipher complex regulatory relationships in living cells. The existing computational approaches often rely on unrealistic biological assumptions and do not explicitly consider signal transduction mechanisms. Signal transduction events refer to linear cascades of reactions from the cell surface to the nucleus and characterize a signaling pathway. In this paper, we propose a novel approach, Gene Set Gibbs Sampling (GSGS), to reverse engineer signaling pathway structures from gene sets related to the pathways. We hypothesize that signaling pathways are structurally an ensemble of overlapping linear signal transduction events which we encode as Information Flows (IFs). We infer signaling pathway structures from gene sets, referred to as Information Flow Gene Sets (IFGSs), corresponding to these events. Thus, an IFGS only reflects which genes appear in the underlying IF but not their ordering. GSGS offers a Gibbs sampling like procedure to reconstruct the underlying signaling pathway structure by sequentially inferring IFs from the overlapping IFGSs related to the pathway. In the proof-of-concept studies, our approach is shown to outperform the existing state-of-the-art network inference approaches using both continuous and discrete data generated from benchmark networks in the DREAM initiative. We perform a comprehensive sensitivity analysis to assess the robustness of our approach. Finally, we implement GSGS to reconstruct signaling mechanisms in breast cancer cells.
Bioinformatics, Educational institutions, Computational biology, Joints, USA Councils, Computer science, Aerospace electronics

L. Acharya, T. Judeh, Zhansheng Duan, M. Rabbat and Dongxiao Zhu, "GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 438-450, 2012.
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