This program uses the TRANSFAC public database, which contains an extensive compilation of published binding site data for eukaryotic transcription factors, their experimentally proven binding sites and regulated genes.
To determine the TFBS density, we used a compilation of 80 binding sites represented by International Union for Pure and Applied Chemistry consensus sequences (Gasch et al. 2004).
TF, Transcription Factors DBD, DNA-Binding Domain HMMs, Hidden Markov Models SCOP, Structural Classification of Proteins HTH, Helix-Turn-Helix TUs, Transcriptional Units Crp, CcpA, Crc, Catabolite response regulators σ, Sigma factor S. M-C carried out the compilation of DNA-binding TFs from diverse DBs.
I used publically available compilations of characterized binding sites for Bcd and Kr [ 33, 45] to construct specificity matrices using a pseudocount of 1 per position.
References. 1. Bietz S, Rarey M. SIENA: Efficient compilation of selective protein binding site ensembles.
In fact, we offer here the most comprehensive compilation of phylogenetically conserved binding sites and epigenomics predictions in the fruit fly genome published to date.
Unique compilation of the internationally-binding standards and recommendations for chemistry and related fields created by the International Union of Pure and Applied Chemistry IUPACC).
IUPAC Standards Online Database Unique compilation of the internationally-binding standards and recommendations for chemistry and related fields created by the International Union of Pure and Applied Chemistry IUPACC).
A compilation of the data characterizing the DNA-binding transcriptional regulators of each species is provided as supplementary material (see Additional files 1, 2, 3 and 4).
Attempts to find common characteristics for protein-protein recognition sites have only been moderately successful, since the average binding epitope of a large compilation of protein-protein interfaces is almost indistinguishable from a regular protein surface [ 51].
