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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 .
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
*
A/T/C/G
1 bp
Alt
*
A/T/C/G
1 bp
hypothesis
*
Select a hypothesis
Gain of function
Loss of function
Both
Add Row
Choose TF Reference Data
Relative Affinity
motifs/PWMs
*
Input one of the following TF datasets:
Do not use relative affinity
All TFs
Enter your own TFs
Select TFs within tissues
Select all TFs from dataset using the selected normalization.
Affinity Normalization
Signal-to-noise
Relative
TF Family
*
Select TF family.
TF PBM Dataset
*
Select TF PBM dataset.
Core Site
*
IUPAC formatted core binding site.
Affinity Normalization
*
Select normalization method.
Select family
Select dataset
Select core site
Signal-to-noise
Relative
Add Row
Select Organism
Select Time
Select Organ
Select Cell
Add Selection
Groups
TFs to Analyze
Affinity Normalization
Signal-to-noise
Relative
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.
*
Select PWM annotation method:
Do not use PWMs
All TFs
Selected TFs based on keywords
Subset TFs based on expression data
database to use
Either JASPAR or HOCOMOCO.
Choose Database
Jaspar Vertebrates 2024
HOCOMOCO13 Core Motifs
download example
Select Organism
Select Family
Select Type
Select Factor
Add Selection
Selected Motif Categories
Motifs to Include
List of keywords to filter
Keywords to indicate which PWMs to filter for. Keywords can either be TF name, family, or matrix ID.
Select Organism
Select Time
Select Organ
Select Cell
Add Selection
Groups
TFs to Analyze
Affinity Normalization
Signal-to-noise
Relative
Background nucleotide frequencies
What background frequencies of nucleotides. Description of background frequencies here.
Human genome
Mouse genome
Choose your own
A:
T:
G:
C:
Pwm minimum score
Enter the minimum PWM score required for analysis. Default is 0.8.
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.
Submit