Simultaneous reconstruction of multiple signaling pathways via the prize collecting Steiner forest problem

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2012_Book_ResearchInComputationalMolecul_303-317.pdf

Date

2012-04-13

Author

Tunçbağ, Nurcan
PAGNANI, ANDREA
HUANG, SHAO SHAN CAROL
CHAYES, JENNIFER
BORGS, CHRISTIAN
ZECCHINA, RICCARDO
FRAENKEL, ERNEST

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Signaling networks are essential for cells to control processes such as growth and response to stimuli. Although many “omic” data sources are available to probe signaling pathways, these data are typically sparse and noisy. Thus, it has been difficult to use these data to discover the cause of the diseases. We overcome these problems and use “omic” data to simultaneously reconstruct multiple pathways that are altered in a particular condition by solving the prize-collecting Steiner forest problem. To evaluate this approach, we use the well-characterized yeast pheromone response. We then apply the method to human glioblastoma data, searching for a forest of trees each of which is rooted in a different cell surface receptor. This approach discovers both overlapping and independent signaling pathways that are enriched in functionally and clinically relevant proteins, which could provide the basis for new therapeutic strategies.

Subject Keywords

Prize-collecting Steiner forest, Signaling pathways, Multiple network reconstruction

URI

https://hdl.handle.net/11511/30132

DOI

https://doi.org/10.1007/978-3-642-29627-7_31

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Graduate School of Informatics, Conference / Seminar

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Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem Tunçbağ, Nurcan; PAGNANI, Andrea; Huang, Shao-Shan Carol; CHAYES, Jennifer; BORGS, Christian; Zecchina, Riccardo; FRAENKEL, Ernest (2013-02-01) Signaling and regulatory networks are essential for cells to control processes such as growth, differentiation, and response to stimuli. Although many "omic'' data sources are available to probe signaling pathways, these data are typically sparse and noisy. Thus, it has been difficult to use these data to discover the cause of the diseases and to propose new therapeutic strategies. We overcome these problems and use "omic'' data to reconstruct simultaneously multiple pathways that are altered in a particula...
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Stochastic modelling of the MAPK signalling pathway Purutçuoğlu Gazi, Vilda (null; 2006-06-01) The MAPK (mitogen-activated protein kinase) or its synonymous ERK (extracellular signal regulated kinase) pathway whose components are Ras, Raf, and MEK proteins with many biochemical links, is one of the major signalling systems involved in cellular growth control of eukaryotes including cell proliferation, transformation, differentiation, and apoptosis. Because of its diverse functionality, it is also activated in a variety of hormone activation and many illnesses, which have multi-complex gene structure ...
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes Arici, M. Kaan; Tunçbağ, Nurcan (2021-10-01) Beyond the list of molecules, there is a necessity to collectively consider multiple sets of omic data and to reconstruct the connections between the molecules. Especially, pathway reconstruction is crucial to understanding disease biology because abnormal cellular signaling may be pathological. The main challenge is how to integrate the data together in an accurate way. In this study, we aim to comparatively analyze the performance of a set of network reconstruction algorithms on multiple reference interac...
Large-Scale Signaling Network Reconstruction Hashemikhabir, Seyedsasan; Ayaz, Eyup Serdar; Kavurucu, Yusuf; Can, Tolga; Kahveci, Tamer (Institute of Electrical and Electronics Engineers (IEEE), 2012-11) Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the existing methods to small signaling networks of size 10-15 genes. In this paper, we propose integrating RNAi data with a reference physical interaction network. We formulate the problem of signaling network reconstruction as finding the minimum number of ed...

Citation Formats

N. Tunçbağ et al., “Simultaneous reconstruction of multiple signaling pathways via the prize collecting Steiner forest problem,” 2012, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/30132.