This amounts to requiring that the similarity between the sets of binding sequences of two TFs comparable to the similarity between the sequences of each TF.
Three binding sequences of CreA protein (5′-SYGGRG-3′) in other fungi were identified in a 1300 bp upstream region of cel7A of A. cellulolyticus (data not shown).
We have identified two Six2 binding sites in the Gdnf promoter that show similarity to the consensus DNA binding sequences of other homeobox proteins and harbor short palindromic sequences.
Iron-deficiency regulated genes may not have highly common cis-elements but they should have one of the binding sequences of IDEF1, IDEF2, OsIRO2 and other TFs regulated by OsIRO2.
Motifs predicted by MAMA, Motif Sampler, MEME, and SIFT from the top 50 genes upregulated by Fe deficiency using default settings, and the binding sequences of IDEF1, IDEF2, and OsIRO2 were used as putative and known cis-elements, respectively.
At the resolution achieved chromosome-wide, we did not find a statistically significant correlation between the predicted binding sequences of the two alleles and recombination rates (Table S5).
The consensus sequence TCCNNNGAA of the IFN-γ-activated site (GAS [13]) does not comprehensively describe all binding sequences of STAT1, but it allows an unbiased assessment of the positional precision of the determination of STAT1 binding in sequence sets.
The empirical binding sequences of the TFs are reported [3], [9] in an extended alphabet (e.g. "rACGCGt" for the transcription factor MBP1) specifying the base preferences or the binding affinities as a set of letters with variable case.
We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a simple "sequence-matching" rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions.
