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Variants in transcription factor binding motifs
Transcription factor binding motifs (TFBMs) are genomic sequences that specifically bind to transcription factors.
The consensus sequence of a TFBM is variable, and there are a number of possible bases at certain positions in the motif, whereas other positions have a fixed base. These are usually illustrated in sequence logo diagrams (Figure 7), where the height of the letter represents how frequently that nucleotide is observed in that position.
Known TFBMs are curated in the JASPAR database.
Due to the variable nature of TFBMs, all motifs found in genomes are given a score out of one, indicating how strong the TFBM is. The score represents the probability of each base occurring at each location in the motif.
If a variant hits a TFBM, it will alter the motif score, making it more or less likely to bind the transcription factor. These variants are called TF binding site variants, and the change in the motif score can be calculated.