A Global Pathway Crosstalk Network

@article{citeulike:2723713, abstract = {Motivation: Given the complex nature of biological systems, pathways often need to function in a coordinated fashion in order to produce appropriate physiological responses to both internal and external stimuli (Hartwell et al., 1999). Therefore, understanding the interaction and crosstalk between pathways is important for understanding the function of both cells and more complex systems. Results: We have developed a computational approach to detect crosstalk among pathways based on protein interactions between the pathway components. We built a global mammalian pathway crosstalk network that includes 580 pathways (covering 4,753 genes) with 1,815 edges between pathways. This crosstalk network follows a power-law distribution: P(k) [\~{}] k-{gamma}, {gamma}= 1.45, where P(k) is the number of pathways with k neighbors, thus pathway interactions may exhibit the same scale-free phenomenon that has been documented for protein interaction networks. We further used this network to understand colorectal cancer progression to metastasis based on transcriptomic data. Contact: yong.2.li@gsk.com 10.1093/bioinformatics/btn200}, author = {Li, Yong and Agarwal, Pankaj and Rajagopalan, Dilip }, citeulike-article-id = {2723713}, doi = {10.1093/bioinformatics/btn200}, journal = {Bioinformatics}, keywords = {cross-talk, functional-genome, genotype-to-phenotype, molecular-signaling, networks, regulatory-cascades}, month = {April}, pages = {btn200+}, posted-at = {2008-06-20 16:14:48}, priority = {2}, title = {A Global Pathway Crosstalk Network}, url = {http://dx.doi.org/10.1093/bioinformatics/btn200}, year = {2008} }

TY - JOUR ID - citeulike:2723713 L3 - citeulike-article-id:2723713 TI - A Global Pathway Crosstalk Network JF - Bioinformatics SP - btn200 N2 - Motivation: Given the complex nature of biological systems, pathways often need to function in a coordinated fashion in order to produce appropriate physiological responses to both internal and external stimuli (Hartwell et al., 1999). Therefore, understanding the interaction and crosstalk between pathways is important for understanding the function of both cells and more complex systems. Results: We have developed a computational approach to detect crosstalk among pathways based on protein interactions between the pathway components. We built a global mammalian pathway crosstalk network that includes 580 pathways (covering 4,753 genes) with 1,815 edges between pathways. This crosstalk network follows a power-law distribution: P(k) [~] k-{gamma}, {gamma}= 1.45, where P(k) is the number of pathways with k neighbors, thus pathway interactions may exhibit the same scale-free phenomenon that has been documented for protein interaction networks. We further used this network to understand colorectal cancer progression to metastasis based on transcriptomic data. Contact: yong.2.li@gsk.com 10.1093/bioinformatics/btn200 KW - cross-talk KW - functional-genome KW - genotype-to-phenotype KW - molecular-signaling KW - networks KW - regulatory-cascades AU - Li, Yong AU - Agarwal, Pankaj AU - Rajagopalan, Dilip PY - 2008/04/23/ UR - http://dx.doi.org/10.1093/bioinformatics/btn200 ER -