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We subdivided mouse promoters based on the presence of CGIs (+/-CGI) and their methylation status [ 5, 32].
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For each PWM, we scored every human and mouse promoter sequence based on maximum log odds scores, and obtained the average of human and mouse homolog promoter scores as the PWM score for each gene.
The PromH scheme identifies promoters based on conservation of regulatory features in pairs of human/mouse orthologous genes.
The sequence of this element is well conserved between human and mouse promoters (16/18 bases), emphasizing its importance for regulation of this gene.
Collagen promoter based transgenic mice, which overexpress LIP in the osteoblast lineage develop osteopenia (Harrison et al, 2005), whereas the L/L k.i.i
The mouse promoter array was based on MM8/mouse genome Build 36 from February 2006 (NimbleGen Systems, Madison, WI).
Although the HXT7 promoter is a glucose-repressible promoter, we select the HXT7 promoter based on its strong expression level especially during the ethanol phase.
Percentages and p-value calculations are based on mouse promoters.
ATAC-seq revealed that in NMR, promoters of reprogramming genes were more closed than mouse promoters, while expression of LT led to massive opening of the NMR promoters.
In mouse promoters 14 pairs, and in human promoters 2 pairs of PWMs had exceptionally high values, while in mouse promoters 2 pairs had low values.
The corresponding results based on the mouse promoter methylation information were obtained from bisulfite-seq data and are summarized in supplementary figure S3 A – D, Supplementary Material online.
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