Tools | TF Sites

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Compare TF Sites Across Sequences from Genomic Variants

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Take in the genomic coordinates of variants to map how ref/alt sequence changes impact the function of TF binding sites. In biomedical applications, comparisons can be made between reference and alternate alleles that are associated with diseases or changes in gene expression.

Links: Tutorial Video Documentation

Enter Genetic Variant Information

Analysis name* Provide a name for this analysis.

Genome* Pickled genome file that corresponds to the genomic coordinates provided. This is used to extract the sequences to be compared. Start by selecting one of our genomes or uploading your own .

Variants* Tab-separated file containing the list of genomic coordinates to analyze. There should be at least 5 columns in this file, including the chromosome, position, reference allele, alternate allele, and hypothesis (values can include gof/lof/both/na).

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Tab-separated, 5 columns: chr, pos, ref, alt, hypothesis.
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chrom*	Pos*	Ref* A/T/C/G 1 bp	Alt* A/T/C/G 1 bp	hypothesis*

Choose TF Reference Data

Relative Affinity
motifs/PWMs

*Input one of the following TF datasets:

*Select PWM annotation method:

List of keywords to filter Keywords to indicate which PWMs to filter for. Keywords can either be TF name, family, or matrix ID. Keywords lacking data will be reported in output table.

Exact keyword match Require the exact keyword to match (e.g. SOX1 will return SOX1 but not SOX11). If unselected, TF families can be more easily searched for (e.g. ETS will return ETS1, ETS2, etc).

Pwm minimum score Enter the minimum PWM score required for analysis. Default is 0.8.

Use pseudoweights Whether to use pseudoweights to handle zero values in a position frequency matrix (PFM). They will be calculated using the standard method √N × b (N = number of sequences and b = background nucleotide frequency).

Other Parameters

position index type* 1 if the provided position coordinates are one-indexed and 0 if they are zero-indexed.

window size* Length of the binding sites that are being analyzed. This will be used to determine the number of nucleotides to include on each side of a variant when extracting the surrounding sequence

Minimum binding change* Enter the minimum binding change threshold for analysis.