Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis Export

@article{citeulike:5887125, abstract = {10.1073/pnas.0305287101 Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators bind to or dissociate from DNA, respectively, and modulate transcriptional activities on particular promoters. Traditionally, individual reporter genes have been used to detect the activity of the transcription factors. This approach works well for simple, non-overlapping transcription pathways. For complex transcriptional networks, more sophisticated tools are required to deconvolute the contribution of each regulator. Here, we demonstrate the utility of network component analysis in determining multiple transcription factor activities based on transcriptome profiles and available connectivity information regarding network connectivity. We used carbon source transition from glucose to acetate as a model system. Key results from this analysis were either consistent with physiology or verified by using independent measurements.}, author = {Kao, Katy C. and Yang, Young-Lyeol and Boscolo, Riccardo and Sabatti, Chiara and Roychowdhury, Vwani and Liao, James C.}, citeulike-article-id = {5887125}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0305287101}, citeulike-linkout-1 = {http://www.pnas.org/content/101/2/641.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/101/2/641.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/14694202}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=14694202}, day = {13}, doi = {10.1073/pnas.0305287101}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {component, factor-analysis, network, regulators, transcription, transcriptome}, month = {January}, number = {2}, pages = {641--646}, posted-at = {2009-10-04 16:51:37}, priority = {2}, title = {Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis}, url = {http://dx.doi.org/10.1073/pnas.0305287101}, volume = {101}, year = {2004} }

TY - JOUR ID - citeulike:5887125 L3 - citeulike-article-id:5887125 N2 - 10.1073/pnas.0305287101 Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators bind to or dissociate from DNA, respectively, and modulate transcriptional activities on particular promoters. Traditionally, individual reporter genes have been used to detect the activity of the transcription factors. This approach works well for simple, non-overlapping transcription pathways. For complex transcriptional networks, more sophisticated tools are required to deconvolute the contribution of each regulator. Here, we demonstrate the utility of network component analysis in determining multiple transcription factor activities based on transcriptome profiles and available connectivity information regarding network connectivity. We used carbon source transition from glucose to acetate as a model system. Key results from this analysis were either consistent with physiology or verified by using independent measurements. IS - 2 JF - Proceedings of the National Academy of Sciences of the United States of America EP - 646 TI - Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis VL - 101 SP - 641 KW - component KW - factor-analysis KW - network KW - regulators KW - transcription KW - transcriptome AU - Kao, Katy AU - Yang, Young-Lyeol AU - Boscolo, Riccardo AU - Sabatti, Chiara AU - Roychowdhury, Vwani AU - Liao, James PY - 2004/01/13/ UR - http://dx.doi.org/10.1073/pnas.0305287101 ER -