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Compare TF Sites across 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
Parameters
Analysis name
*
Provide a name for this analysis.
Hypothesis
*
Specify the hypothesis to test. LOF, GOF or both Default is "both".
Enhancer DNA Alignment Table
*
At least two DNA sequences to be analyzed. We suggest only inputting the alignment +/- 15 bp from where the genetic variation of interest occurs. if this is a SNV, you would simply input the 30bp window of the alignment containing the variant. If this is a deletion, you would add 15 bp upstream of the first - and 15bp downstream of the last -.
Manually enter table
Upload a file
download example
DNA Name
*
DNA Alignment
*
Functional Group
*
Add Row
Enhancer Functional Group Table
*
Labels for each functional group. Functional group can be either wild-type, control, test, or na. If na, all enhancers associated with that label will be removed from the analysis. Binding sites are searched for within the test group that are not present within the wild-type or control group. At a minimum both of these requirements must be met, (1) at least one control or wild-type must be provided; (2) at least one test must be provided.
Manually enter table
Upload a file
download example
Group name
*
Group Label
*
wild-type
test
control
na
Add Row
*
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.
Submit