This folder contains data files used in the analysis described in the manuscript by Alam et al., currently being prepared for submission. Folder MotifActivity contains the scripts to calculate motif activities from expression data. See the README file in that folder for a detailed explanation of the scripts. Whole-genome transcription factor binding site predictions to be used with these scripts are provided as described below. Folder TFBS contains transcription factor binding site predictions generated by MotEvo for the whole genome for human genome assembly hg19, mouse genome assembly mm9, rat genome assembly rn6, dog genome assembly canFam3, and chicken genome assemblies galGal5 and galGal6, using whole-genome alignments of human, macaque, mouse, rat, dog, horse, cow, opossum, and chicken. The value in the score column represents the posterior probability of the predicted site. The motifs were obtained from SwissRegulon release of July 13, 2015. Folder MultipleGenomeAlignments contains whole-genome alignments of rat (genome assembly rn6), dog (genome assembly canFam3), and chicken (genome assemblies galGal5 and galGal6), each against the genomes of 29 vertebrate species. The MAF (multiple alignment format) file in each subfolder contains the multiple genome alignments, the .nh (New Hampshire or Newick tree format) file stores the phylogenetic tree, which is visualized in the PDF file. Please see the manuscript for detailed information of the methods used to generate these data sets. Michiel de Hoon, RIKEN Center for Integrative Medical Sciences.
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