Skip to main content

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.