Results from both approaches were then combined to yield a list of sixteen TFs for these eleven genes. From this list we next selected those TFs that were also either activated or suppressed by anti IgM in Figure 2. This exercise resulted in the further short list ing of seven of these TFs. Importantly, the identification of several of these was also supported by experimental evidence in the literature demonstrating their roles in regulating expression of at least some of the target genes. Link ing these seven TFs to the target genes then yielded a dense overlapping regulatory network as shown in Figure 3B. Such a DOR network represents a typical regulatory module that is expected for the regulation of multiple genes by a common set of TFs.
Of the seven TFs described in Figure 3B, TBP, NFKB1, TRP53, and FOSL1 were all activated upon sti mulation of cells with anti IgM. Of these TBP is a component of the general transcription factor TFIID, while both NFKB1 and TRP53 are known regulators of gene expression. Finally, FOSL1 is an oncogene product with a role in tumor formation. Activity of the remaining three TFs MZF1, Sp1, and NFATc2 was, however, suppressed in response to BCR stimulation. Here MZF1 is known for its regulation of apoptosis, whereas NAFTc2 and Sp1 can both act as repressors of gene expression in specific instances. Thus the BCR dependent activation profile of these seven TFs appears to be consistent with the induced expression of the early response genes through the links described in Figure 3B.
Construction of an in silico network that links BCR signaling to gene expression To extract the network of pathways linking BCR acti vation to the cellular response, we first merged the BIND, DIP, IntAct, MINT, Human Dacomitinib Protein Reference Database and Protein Protein interaction database PPI databases to generate a compilation of all known reported PPIs. Eliminating those interactions that lacked experimental support from at least two independent studies then refined the resulting network. This resulted in a core undirected network of about 4300 nodes and 10700 edges. Here the CD79a and CD79b subunits associated with the BCR were taken together and considered as a sin gle BCR complex. Shortest path analysis of networks is generally consid ered to represent a reliable method for capturing infor mation on the transduction of signals through the various intermediate nodes.
Further, our experi ments in Figure 1B had also helped to distinguish at least some of the signaling intermediates that were either significantly activated, or ignored, upon BCR sti mulation of cells. Therefore, starting from the BCR, we next traced all the possible shortest paths leading to each human ortholog of the signaling intermediate that was shown to be activated in Figure 1B.
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