Discovering functional transcription-factor combinations in the human cell cycle Export

@article{citeulike:2537498, abstract = {With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G2-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes. 10.1101/gr.3394405}, author = {Zhu, Zhou and Shendure, Jay and Church, George M.}, citeulike-article-id = {2537498}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.3394405}, citeulike-linkout-1 = {http://www.genome.org/cgi/content/abstract/15/6/848}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/15930495}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=15930495}, day = {1}, doi = {10.1101/gr.3394405}, journal = {Genome Res.}, keywords = {applicationbioinf, combination}, month = {June}, number = {6}, pages = {848--855}, posted-at = {2008-03-15 18:29:23}, priority = {2}, title = {Discovering functional transcription-factor combinations in the human cell cycle}, url = {http://dx.doi.org/10.1101/gr.3394405}, volume = {15}, year = {2005} }

TY - JOUR ID - citeulike:2537498 L3 - citeulike-article-id:2537498 N2 - With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G2-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes. 10.1101/gr.3394405 IS - 6 JF - Genome Res. EP - 855 TI - Discovering functional transcription-factor combinations in the human cell cycle VL - 15 SP - 848 KW - applicationbioinf KW - combination AU - Zhu, Zhou AU - Shendure, Jay AU - Church, George PY - 2005/06/01/ UR - http://dx.doi.org/10.1101/gr.3394405 ER -