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Table 1 Statistics for protein-DNA datasets supplied with DREM 2.0

From: DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Species #TFs #genes Protein-DNA interactions Type Reference
S. cerevisiae 205 6,230 22,167 ChIP-Chip, conservation [34, 35]
E.coli 124 1,763 3,520 curated + computational [26]
D. melanogaster 77 12,504 158,558 ChIP-Chip,ChIP-Seq [8]
M. musculus 336 16,641 468,319 computational prediction,supplement [36]
H. sapiens 127 19,755 954,377 ChIP-Seq [37]
H. sapiens 349 17,848 514,925 computational prediction [36]
A. thaliana 68 8,132 11,354 diverse experimental evidence [38]
  1. Number of protein-DNA interactions for TFs and target genes for the six supplied species H. sapiens, A. thaliana, and M. musculus, S. cerevisiae, and E.coli since DREM 2.0. Higher-confidence subsets of these interactions are also provided for some species. More details can be found in Additional file 2.