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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
Parameters
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 .
Select a genome
hg19 (human)
hg38 (human)
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).
Manually enter table
Upload a file
download example
chrom
*
pos
*
ref
*
alt
*
hypothesis
*
Select a hypothesis
Gain of function
Loss of function
Both
Add Row
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
*
Input one of the following TF datasets:
Analyze with affinity data & core site
Analyze with PWM
TF affinity Information
All the information for the transcription factors being analyzed, including its name, binding site definition, desired color on the plot, any PBM relative affinity data, and any PFM relative score data. You can generate an affinity dataset with the
Normalize TF-DNA Affinity Data
tool.
Manually enter table
Upload info and data files
download example
TF Name
*
Core Site
*
Affinity Data
create an affinity dataset
download example
or
My Affinity datasets
Add Row
tf affinity reference files
File(s) referenced in the TF information file.
download example
Motif input file
*
JASPAR formatted file with multiple PWMs. You can generate a PWM with the
Generate Motif Database
tool.
My Motif databases
or
Choose Preloaded Database
Jaspar Vertebrates 2024
HOCOMOCO13 Core Motifs
or
download example
Pwm minimum score
*
Enter the minimum PWM score required for analysis. Default is 0.8.
Minimum binding change
*
Enter the minimum binding change threshold for analysis.
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