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Our experimental dataset includes measurements for 28 signaling protein phosphorylation states across 16 different factorial combinations of cytokine and matrix stimuli as reported previously.<\/jats:p><jats:p>Results: The Bayesian network modeling approach allows us to uncover previously reported signaling activities related to mouse ES cell self-renewal, such as the roles of LIF and STAT3 in maintaining undifferentiated ES cell populations. Furthermore, the network predicts novel influences such as between ERK phosphorylation and differentiation, or RAF phosphorylation and differentiated cell proliferation. Visualization of the influences detected by the Bayesian network provides intuition about the underlying physiology of the signaling pathways. We demonstrate that the Bayesian networks can capture the linear, nonlinear and multistate logic interactions that connect extracellular cues, intracellular signals and consequent cell functional responses.<\/jats:p><jats:p>Availability: Datasets and software are available online from http:\/\/sysbio.engin.umich.edu\/~pwoolf\/mouseES\/<\/jats:p><jats:p>Contact: \u00a0pwoolf@umich.edu<\/jats:p><jats:p>Supplementary information: \u00a0http:\/\/sysbio.engin.umich.edu\/~pwoolf\/mouseES\/<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti056","type":"journal-article","created":{"date-parts":[[2004,10,13]],"date-time":"2004-10-13T01:32:31Z","timestamp":1097631151000},"page":"741-753","source":"Crossref","is-referenced-by-count":96,"title":["Bayesian analysis of signaling networks governing embryonic stem cell fate decisions"],"prefix":"10.1093","volume":"21","author":[{"given":"Peter J.","family":"Woolf","sequence":"first","affiliation":[]},{"given":"Wendy","family":"Prudhomme","sequence":"additional","affiliation":[]},{"given":"Laurence","family":"Daheron","sequence":"additional","affiliation":[]},{"given":"George Q.","family":"Daley","sequence":"additional","affiliation":[]},{"given":"Douglas A.","family":"Lauffenburger","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,10,12]]},"reference":[{"key":"2023013107224573200_B1","doi-asserted-by":"crossref","unstructured":"Balasubramanian, S., Efimova, T., Eckert, R.L. 2002Green tea polyphenol stimulates a Ras, MEKK1, MEK3, and p38 cascade to increase activator protein 1 factor-dependent involucrin gene expression in normal human keratinocytes. 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