Network motifs in integrated cellular networks of transcriptionâregulation and proteinâprotein interaction Export

@article{citeulike:3594, abstract = {10.1073/pnas.0306752101 Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either transcription\^{a}€“regulation or protein\^{a}€“protein interactions. Here we search for composite network motifs: characteristic network patterns consisting of both transcription\^{a}€“regulation and protein\^{a}€“protein interactions that recur significantly more often than in random networks. To this end we developed algorithms for detecting motifs in networks with two or more types of interactions and applied them to an integrated data set of protein\^{a}€“protein interactions and transcription regulation in . We found a two-protein mixed-feedback loop motif, five types of three-protein motifs exhibiting coregulation and complex formation, and many motifs involving four proteins. Virtually all four-protein motifs consisted of combinations of smaller motifs. This study presents a basic framework for detecting the building blocks of networks with multiple types of interactions.}, address = {Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel.}, author = {Yeger-Lotem, Esti and Sattath, Shmuel and Kashtan, Nadav and Itzkovitz, Shalev and Milo, Ron and Pinter, Ron Y. and Alon, Uri and Margalit, Hanah}, citeulike-article-id = {3594}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0306752101}, citeulike-linkout-1 = {http://www.pnas.org/content/101/16/5934.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/101/16/5934.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/101/16/5934}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15079056}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15079056}, day = {20}, doi = {10.1073/pnas.0306752101}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {biology, dynamics, feedback, genetic, motif, network}, month = {April}, number = {16}, pages = {5934--5939}, posted-at = {2009-11-02 22:04:35}, priority = {2}, title = {Network motifs in integrated cellular networks of transcription\^{a}€“regulation and protein\^{a}€“protein interaction}, url = {http://dx.doi.org/10.1073/pnas.0306752101}, volume = {101}, year = {2004} }

TY - JOUR ID - citeulike:3594 L3 - citeulike-article-id:3594 N2 - 10.1073/pnas.0306752101 Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either transcription–regulation or protein–protein interactions. Here we search for composite network motifs: characteristic network patterns consisting of both transcription–regulation and protein–protein interactions that recur significantly more often than in random networks. To this end we developed algorithms for detecting motifs in networks with two or more types of interactions and applied them to an integrated data set of protein–protein interactions and transcription regulation in . We found a two-protein mixed-feedback loop motif, five types of three-protein motifs exhibiting coregulation and complex formation, and many motifs involving four proteins. Virtually all four-protein motifs consisted of combinations of smaller motifs. This study presents a basic framework for detecting the building blocks of networks with multiple types of interactions. IS - 16 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel. EP - 5939 TI - Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction VL - 101 SP - 5934 KW - biology KW - dynamics KW - feedback KW - genetic KW - motif KW - network AU - Yeger-Lotem, Esti AU - Sattath, Shmuel AU - Kashtan, Nadav AU - Itzkovitz, Shalev AU - Milo, Ron AU - Pinter, Ron AU - Alon, Uri AU - Margalit, Hanah PY - 2004/04/20/ UR - http://dx.doi.org/10.1073/pnas.0306752101 ER -