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Visualize TF Sites on Sequences
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Predict and visualize TF binding sites on one or multiple enhancers. Sites can be predicted using two approaches. The first and preferred is to predict sites with a core binding site and determine binding site affinity using a reference affinity dataset. When less studies on the TF have been performed, the alternative approach is to use a PWM to predict locations and binding scores. The output is (1) an image visualizing where the predicted sites are along with their affinity or PWM-binding score, and (2) a table with every binding site, its location, direction, affinity and a unique site identifier.
Links:
Tutorial Video
Documentation
Enter Enhancer DNA sequence(s)
DNA sequence(s) to annotate
One or more named DNA sequences to be annotated.
Manually enter table
Upload a file
download example
Sequence name
*
Name of the Enhancer.
Sequence
*
DNA Sequence of the Enhancer. Only use upper case A/T/C/G.
Add Row
Annotate TF with relative affinity
Do not use relative affinity
Enter your own TFs
Select TFs within tissues
TF Family
*
Select TF family.
TF PBM Dataset
*
Select TF PBM dataset.
Core Site
*
IUPAC formatted core binding site.
Affinity Normalization
*
Select normalization method.
Color
*
color options
Color of the predicted TFBS plotted.
Minimum Affinity
Threshold affinity of predicted TFBS to keep.
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
Annotate TF with PWM binding scores
*
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
Required PWM score to predict a site. Does not apply to PWMs referenecd in the "tf information tsv" file. Default is 0.7.
Pwm binding site color
Color of sites for PWMs. Default is grey.
Other Parameters
Output images as SVG
Option to output images as SVG in addition to PNG. SVG are preferable for manuscript preparation.
True
False
Plot resolution
Enter the resolution for the plot in DPI (dots per inch).
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.
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