Table 1.

Components and notations of the CNEReg model

Data and variable	Notation	Example
Expression of TTFs	$\mathit{TT}{F}_{l,t}$ = expression of the l-th TTF on t-th time point	$\mathit{TT}{F}_{HOXC8}$ = 25.48 on D7 in rumen
Expression of TFs	$T{F}_m$ = expression of the m-th TF	$T{F}_{\mathit{JUN}}$ = 1035.79 on D7 in rumen
Expression of RSEGs	$\mathit{RSE}{G}_{n,t}$ = expression of the n-th RSEG on t-th time point	$\mathit{RSE}{G}_{SLC14A1}$ = 42.34 on D7 in rumen
Accessibility of active-RSCNEs	$O_{k,t}$ = openness of the k-th active-RSCNE on t-th time point	$O_{\mathrm{Chr}1:196579342-242}$ = 18.83 on D7 in rumen
TFs with motif match in an active-RSCNE	${\mathit{MB}}_{i,l}$ = the set of TFs with significant motif match in i-th active-RSCNE	HOXC8 has motif match at active-RSCNE Chr1:196579342–242
Motif matching strength of TFs on RSCNEs	$B_{i,l}$ = sum of −log P value of l-th TF’s motif on i-th active-RSCNE	$B_{\mathrm{Chr}1:196579342-242}$ = 4.28486

Note: CNEReg, conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network; TTF, toolkit transcription factor; TF, transcription factor; RSEG, rumen-specific expressed gene; RSCNE, ruminant-specific conserved non-coding element.