TY - GEN
T1 - Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem
AU - Tuncbag, Nurcan
AU - Braunstein, Alfredo
AU - Pagnani, Andrea
AU - Huang, Shao Shan Carol
AU - Chayes, Jennifer
AU - Borgs, Christian
AU - Zecchina, Riccardo
AU - Fraenkel, Ernest
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
KW - Prize-collecting Steiner forest
KW - multiple network reconstruction
KW - signaling pathways
UR - http://www.scopus.com/inward/record.url?scp=84860818102&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84860818102&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-29627-7_31
DO - 10.1007/978-3-642-29627-7_31
M3 - Conference contribution
AN - SCOPUS:84860818102
SN - 9783642296260
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 287
EP - 301
BT - Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings
T2 - 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012
Y2 - 21 April 2012 through 24 April 2012
ER -