Table 1.

Model components

Description of data and variablesNotationExample
Context-dependent data
 Expression of TFTFk := expression of kth TFTFJun = 94.9 in lung
 Expression of CRCRj := expression of jth CRCREp300 = 19.4 in lung
 Expression of TG, not TF/CRTGl := expression of lth TGTGKrt8 = 86.1 in lung
 Accessibility of REOi := degree of openness of ith REOchr4:94,821,700–94,824,600 = 5.45 in lung
Context-dependent latent variable
 Activity status of REZi := indicator for whether ith RE is activeRE at chr4:94,821,700–94,824,600 is active in lung
 Binding status of CR in RECi,j := indicator for whether jth CR is recruited to ith REHdac2 binds RE at Chr4:94,821,700–94,824,600 in lung
Non–context-dependent data
 Interacting TFs for a CRPPI(CRj) := set of TFs known to interact with jth CRPPI(Hdac2) contains Creb3l1
 TFs with motif match in a REMBi := set of TFs with significant motif match in ith REPou4f1 has motif match at RE chr4:94,567,400–94,568,400
 Motif matching strength of TF on REBi,k := sum of −log(P value) of kth TF's motif on ith REBchr4:94,821,700–94,824,600, Sox8 = 12.61