What is TFBSshape?

TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs). These structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. The DNA shape features were predicted using our recently published high-throughput method (Zhou et al. NAR 2013) and visualized in the form of heat maps. Users can download these DNA shape feature data and perform further analysis, for example, to identify which DNA shape feature(s) at which position(s) in the target DNA contribute to the DNA binding specificity of a TF. Users can also compare DNA shape profiles, both qualitatively and quantitatively, between two TF datasets from the database, or between a set of uploaded sequences and a TF from the database.

Figure 1

JASPAR

32 Species
101 TF Families
955 TFs

UniPROBE

26 Species
78 TF Domains
627 TFs

EpiSELEX-seq

7 TFs
in-vitro methylation

MeDReaders

175 TFs
in-vivo methylation
 Citing TFBSshape
New Version (2019)
T.P. Chiu, B. Xin, N. Markarian, Y. Wang, and R. Rohs. (2019) TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. Nucleic acids research, gkz970.

Original Version (2014)
L. Yang, T. Zhou, I. Dror, A. Mathelier, W.W. Wasserman, R. Gordân, and R. Rohs. (2014) TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic acids research, 42, D148-D155.