Tools | TF Sites

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Predict Effects of SNVs on TF Sites

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Predict and visualize the effect of every possible mutation within an enhancer sequence on TF binding. For mutations within predicted sites in the wild-type sequence, the mutation can either have no effect, decrease, optimize or ablate the TF-DNA interactions as quantified by either PWM-binding score or affinity reference dataset. For mutations residing outside predicted sites in the wild-type sequence, the mutation can either have no effect or create a de novo binding site, whose strength of interaction is again quantified either PWM-binding score or affinity reference dataset. If a mutation has multiple effects on TF binding, all effects are reported. When available, use of a binding site core and reference affinity dataset are always preferred over PWM approaches, as PWM-binding scores are worse predictors of binding affinity.

Links: Tutorial Video Documentation

Enter Enhancer DNA sequence(s)

DNA sequence(s) to annotate* One or more DNA sequences to perform in silico mutagenesis on.

Manually enter table

Upload a file

Upload Sequences
Upload BED Regions

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BED Regions File BED file containing genomic regions to annotate (chr, start, end, name).

Genome* Reference genome for the BED coordinates. Select a genome or enter a URL.

DNA Name* Name of the Enhancer.	DNA Sequence* DNA sequence of the Enhancer. Only A/T/C/G characters allowed (lowercase will be converted to uppercase). Maximum 2000 characters.
	0/2000 characters Maximum 2000 characters allowed Only A, T, C, G characters allowed. Invalid characters filtered automatically.

Tf name* Name of the transcription factor being analyzed.

Enter Transcription Factor to Analyze

TF Family* Select TF family.	TF PBM Dataset* Select TF PBM dataset.	Core Site* IUPAC formatted core binding site.	Affinity Normalization ?* Select normalization method.

Add new Normalized tfsite and core to community generated data.

Search for JASPAR motif Search for and select JASPAR motifs to analyze (e.g. type "ETS" to find Ets1)

Selected motif:

PWM Database Select the PWM database to use for motif searching.

Background nucleotide frequencies Select background frequencies for PWM scoring.

Custom Background Frequencies Enter custom background nucleotide frequencies (must sum to 1.0).

Pwm minimum score Minimum score for PWM to predict a site.

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).

Core binding site definition* IUPAC definition of the core transcription factor binding site.

TF Family

Core Site Type

Core Site

Other Parameters

Output images as SVG Option to output images as SVG in addition to PNG. SVG are preferable for manuscript preparation.

SNV Type Effect to Report* Select the types of SNV effects to report.

Optimize

Reduce

De Novo

Ablation

Affinity optimization threshold If using relative affinity or signal-to-noise, only SNVs with a fold change above this threshold will be reported. If using e-score, this value will be delta rather than fold change. By default, all SNVs will be reported.

Affinity reduction threshold If using relative affinity or signal-to-noise, only SNVs with a fold change below this threshold will be reported. If using e-score, this value will be delta rather than fold change. By default, all SNVs will be reported.

Plot resolution Resolution of the plot, in dots (pixels) per inch. Manuscripts require 300 dpi. Dpi does not effect resolution of SVG.

Zoom range Optional: Given a start position and an end position, zoom into a portion of the sequence. The numbers in the range are inclusive. For example, the first 200 nucleotides of the sequence would be specified as: 1-200. Leave blank if not applicable.