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. Author manuscript; available in PMC: 2012 Aug 1.
Published in final edited form as: Trends Cell Biol. 2011 May 31;21(8):442–451. doi: 10.1016/j.tcb.2011.05.001

Figure 2.

Figure 2

Example of a Transcriptional Regulatory Network Reconstruction Components of transcriptional networks include transcription factors (TFs) and their target genes (circles); connections between them (lines between circles) denote binding of a TF to the regulatory region of a target gene. If this TF binding results in gene expression changes, then this connection is a regulatory connection; reconstruction of this results in a transcriptional regulatory network (TRN). (a, left) Schematic drawing of the upstream and coding region of a gene (gene B). Predicted or experimentally determined TF binding sites (gray boxes) of TF A are found in the upstream region of gene B. (a, right) This information can be used to reconstruct a representation of the connection (gray line) between a TF A (gray outlined circle A) and its target gene B (gray outlined circle B). (b) The process in (a) can be performed iteratively for each TF and gene in the genome. These can then be assembled to reconstruct a TRN representation. This TRN reconstruction does not include gene expression information, thus this network looks the same in cell states 1 and 2. (c) From Figure 1, a schematic drawing of a cellular transition. It serves as a reference for the networks in (b) and (e). (d, left) Same representation and case as in (a), except there is also gene expression data supporting the expression of TF A (orange circle with green outline) and corresponding changes in the expression levels of its target (gene B, orange circle with blue outline). The orange arrow with blue outline indicates activation of gene B due to binding and regulation by TF A. (d, right) A representation of the relationship between TF A and gene B. TF A action (orange circle with a green outline) results in expression of target gene B (orange circle with a blue outline). The blue line represents the relationship between them, which is a regulatory connection. (e) The process in (d) can be performed iteratively for each TF and gene in the genome for each cell state. These can be assembled to reconstruct a TRN representation for cell states 1 (left) and 2 (right). Note that components (A and B) and regulatory connections in (d) are absent in cell state 1 (left), but present after the cellular transition to cell state 2 (right). The black vertical line labeled TSS in (a) and (d) denotes the Transcriptional Start Site of gene B.