Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks Export

@article{citeulike:5201306, abstract = {Motivation: Spatio-temporal regulation of gene expression is an indispensable characteristic in the development processes of all animals. Master switches', a central set of regulatory genes whose states (on/off or activated/deactivated) determine specific developmental fate or cell-fate specification, play a pivotal role for whole developmental processes. In this study on genome-wide integrative network analysis the underlying design principles of developmental gene regulatory networks are examined. Results: We have found an intriguing design principle of developmental networks: hub nodes, genes with high connectivity, equipped with positive feedback loops are prone to function as master switches. This raises the important question of why the positive feedback loops are frequently found in these contexts. The master switches with positive feedback make the developmental signals more decisive and robust such that the overall developmental processes become more stable. This finding provides a new evolutionary insight: developmental networks might have been gradually evolved such that the master switches generate digital-like bistable signals by adopting neighboring positive feedback loops. We therefore propose that the combined presence of positive feedback loops and hub genes in regulatory networks can be used to predict plausible master switches. Contact: ckh@kaist.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp316}, author = {Seo, Chang H. and Kim, Jeong-Rae and Kim, Man-Sun and Cho, Kwang-Hyun}, citeulike-article-id = {5201306}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp316}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/15/1898}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19439566}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19439566}, day = {1}, doi = {10.1093/bioinformatics/btp316}, journal = {Bioinformatics}, keywords = {complexity, development, gene, hub, interaction, network, transcription}, month = {Aug}, number = {15}, pages = {1898--1904}, posted-at = {2009-08-11 17:03:45}, priority = {2}, title = {Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks}, url = {http://dx.doi.org/10.1093/bioinformatics/btp316}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:5201306 L3 - citeulike-article-id:5201306 N2 - Motivation: Spatio-temporal regulation of gene expression is an indispensable characteristic in the development processes of all animals. Master switches', a central set of regulatory genes whose states (on/off or activated/deactivated) determine specific developmental fate or cell-fate specification, play a pivotal role for whole developmental processes. In this study on genome-wide integrative network analysis the underlying design principles of developmental gene regulatory networks are examined. Results: We have found an intriguing design principle of developmental networks: hub nodes, genes with high connectivity, equipped with positive feedback loops are prone to function as master switches. This raises the important question of why the positive feedback loops are frequently found in these contexts. The master switches with positive feedback make the developmental signals more decisive and robust such that the overall developmental processes become more stable. This finding provides a new evolutionary insight: developmental networks might have been gradually evolved such that the master switches generate digital-like bistable signals by adopting neighboring positive feedback loops. We therefore propose that the combined presence of positive feedback loops and hub genes in regulatory networks can be used to predict plausible master switches. Contact: ckh@kaist.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp316 IS - 15 JF - Bioinformatics EP - 1904 TI - Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks VL - 25 SP - 1898 KW - complexity KW - development KW - gene KW - hub KW - interaction KW - network KW - transcription AU - Seo, Chang AU - Kim, Jeong-Rae AU - Kim, Man-Sun AU - Cho, Kwang-Hyun PY - 2009/Aug/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp316 ER -