NFI family of DNA binding proteins preferentially binds upstream of initiation sites of transcription in mouse genome. A set of 61,492 NFI predicted sites was defined in the mouse genome, NCBI build 37 or mm9. Sites were defined with a previously established position weight matrix (sequence score threshold > 85, out of maximum 100) . Within this set, 2,852 predicted sites overlapped regions 5 kb upstream from RefSeq annotated transcriptional start sites (TSS). As a negative control for this experiment, a complementary dataset of 58,640 sites was selected (panel A) or the same number of NFI predicted sites (2,852) were randomly selected from the initial set of 61,492 predicted sites (panel B). Four independently performed random selection are shown. Average NFI ChIP-Seq tag counts were calculated in windows of 50 bp for a region of 5 kb up- and down-stream of the selected NFI predicted sites. Tag counts were normalized globally, as a fold increase over the genome average tag count in a window of 50 bp. Obtained data points were connected to form a continuous line.
Pjanic et al. BMC Genomics 2011 12:181 doi:10.1186/1471-2164-12-181