Therefore, a good database for plant TFs and transcription factor binding sites (TFBSs) will be useful for starting a series of complex experiments. In this chapter, PlantPAN (version 3.0) is utilized as an example to explain how bioinformatics systems advance research on gene regulation....
Unification of independent collection of transcription factor binding sites and motifs. YeasTracthttp://www.yeastract.com/ Yeast-specific database. Factors, binding sites and motifs + tools. FlyReghttp://www.flyreg.org/ Drosophila DNase I Footprint Dat...
First, when the context only involves a single gene, the phrase means a short DNA sequence (typically 4鈥 30 base pairs long), which is typically located within a short distance upstream of the associated gene, and is specifically recognized by a transcription factor to control the expression ...
Overall, we found 111 transcription factor pairs (representing ~36% of the total interactions; One-way ANOVA, Bonferroni-corrected) showing highly significant differences in expression due to orientation (Fig. 3c-d, Supplementary Data 1). We also note that 34 of these also showed statistically ...
Generation of the altered TF binding site database To predict the effect of all possible SNVs in the human genome on TF binding, for each possible SNV and each TF with available PWMs, we calculated the binding score for the reference and alternate SNV alleles. We downloaded 1898 PWMs corre...
Scientists routinely scan DNA sequences for transcription factor (TF) bindingsites (TFBSs). Most of the available tools rely on position-specific scoringmatrices (PSSMs) constructed from aligned binding sites. Because of theresolutions of assays used to
Finally, we identified 1288 putative TFs from 21 cyanobacterial genomes, among which 404 genes have not been annotated as transcriptional factor (including neither shown the function of regulation, nor possessing the helix-turn-helix motif) in its original annotation in the IMG database. Some ...
conducive in one orientation, silent in the other. fig. 1 schematic illustration of the consequences of the orientation reversal of an hypothetical, non-palindromic cis-regulatory transcription factor binding site motif. as the motif sequence is reversed in sequence direction on the opposing strand ...
All remaining domains were represented by profile-HMMs downloaded from the PFAM database. This figure is accessible via the Plant Transcription Factor Database http://plntfdb.bio.uni-potsdam.de/v1.0/rules.php, and links are provided to the respective TF families and domains. Full size image ...
Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation Said et al. used cryoEM, biochemistry and bioinformatics to uncover how the Sm-like protein Rof regulates transcription termination. Rof binds termination factor ρ, inhibiting ρ ...