Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the Genome

[Column E and Column F] We overlapped the location coordinates of the 81,922 0-nt to 5-nt variant 13-nt ERE or HRE DNA elements in the genome and the location coordinates of the ChIPSeq or ChIPExo peaks in an experiment (157 ER experiments at 0-nt to 5-nt variant ERE DNA elements) (194 KR experiments at 0-nt to 5-nt variant HRE DNA elements) to determine the absolute number of times each 0-nt to 5-nt variant 13-nt ERE or HRE DNA element occurred within an experiment (the entire 13-nt DNA element was required to be within the peak boundaries). [Column V] Multiple peak selection criteria were used (L4, L8, L10, L15, L20), where Lx represents an x-fold greater tag density at peaks than in the surrounding 10-kb region. This performs a low-to-high stringency analysis of the data. By studying the data with respect to a multiple spectrum of peak selection criteria, we adjust for both the risk of excess background noise and the risk of filtering out any low-amplitude information. All peaks are observed at L4, [Column V] identifies whether that specific peak is also observed at L8, L10, L15 or L20. The ChIPSeq or ChIPExo peaks were annotated to regions in the genome (annotatePeaks.pl) using Homer. [Column A] Peak ID [Column B] Chromosome [Column C] Peak start position [Column D] Peak end position [Column G] Strand [Column H] Peak Score [Column I] FDR/Peak Focus Ratio/Region Size [Column J] Annotation (i.e. Exon, Intron, ...) [Column K] Detailed Annotation (Exon, Intron etc. + CpG Islands, repeats, etc.) [Column L] Distance to nearest RefSeq TSS [Column M] Nearest TSS: Native ID of annotation file [Column N] Nearest TSS: Entrez Gene ID [Column O] Nearest TSS: Unigene ID [Column P] Nearest TSS: RefSeq ID [Column Q] Nearest TSS: Ensembl ID [Column R] Nearest TSS: Gene Symbol [Column S] Nearest TSS: Gene Aliases [Column T] Nearest TSS: Gene description [Column U] Nearest TSS: Gene type