TFbindingMode | Help Documentation

Homepage Browser Tool Prediction Methods Sequence Input File Upload

1. Homepage Interface

1.1 Navigation Bar

Home: Return to main website
Data Query: Access cross-species prediction database
Prediction: Navigate to TF-nucleosome prediction tool
Help: View documentation

1.2 Main Modules

Cross-species prediction results: Click "Start Exploring" to query database
Online Prediction: Click "Start Prediction" to access prediction tool

Figure 1: Website homepage interface

2. TF-nucleosome Browser

Click search box or dropdown to display 30 species. Select target species and click Query to view predictions.

Select All: Check all predictions for selected species
Export: Download results locally (Filename format: result_species_timestamp)

Figure 2: TF-nucleosome browser interface

3. TF-nucleosome Interaction Prediction

Two prediction methods available:

Text input: Directly enter protein sequences in text box

File upload: Upload FASTA format sequence files

3.1 Sequence Input

Input format: Protein sequences (Multiple sequences supported, see example)
Clear Input: Reset all input content
Run Prediction: Execute prediction on input sequences
Example sequences used if input is empty
Select All: Check all prediction results
Download: Export results locally (Filename format: Prediction_input-fast_timestamp)

Example Format

>Protein_001
MAHVSSETQDVSPKDEL...
>Protein_002
MDEDEFELQPQEPNSFF...

Figure 3: Sequence input interface

3.2 File Upload

Format requirements: FASTA formatted protein sequence file
File size: Maximum 10MB
Run Prediction: Execute prediction on uploaded sequences
Select All: Check all prediction results
Download: Export results locally (Filename format: Prediction_filename_timestamp)
Download example file for format reference

Figure 4: File upload interface

Result Interpretation Guide

Figure 5: Prediction results interface

Prediction Metrics Explained

Metric	Interpretation
TF ID (Transcription Factor Identifier)	Unique identifier of a transcription factor (e.g. ENSAMEP00000031528.1)
End Prob (End-binding Probability)	Probability of the TF binding to nucleosomes via end-binding mode. Values approaching 1 indicate higher probability, while values approaching 0 indicate lower probability.
End Label (End-binding Prediction Label)	Predicted label of End-binding mode by using a probability threshold of 0.5. Yes indicates the TF adopts end-binding mode, while No indicates the TF does not adopt end-binding mode.
Groove Prob (Groove-binding Probability)	Probability of the TF binding to nucleosomes via groove-binding mode. Values approaching 1 indicate higher probability of binding to DNA major groove, while values approaching 0 indicate higher probability of binding to DNA minor groove.
Groove Label (Groove-binding Prediction Label)	Predicted label of groove-binding mode by using a probability threshold of 0.5. Major indicates the TF binds to DNA major groove, while Minor indicates the TF binds to DNA minor groove.
Periodic Prob (Periodic-binding Probability)	Probability of the TF binding to nucleosomes via periodic-binding mode. Values approaching 1 indicate higher probability, while values approaching 0 indicate lower probability.
Periodic Label (Periodic-binding Prediction Label)	Predicted label of Periodic-binding mode by using a probability threshold of 0.5. Yes indicates the TF adopts periodic-binding mode, while No indicates the TF does not adopt periodic-binding mode.
Stability Prob (Nucleosome-Stability Regulation Probability)	Probability of regulating nucleosome stability via TF binding. Values approaching 1 indicate higher probability of stabilizer, while values approaching 0 indicate higher probability of destabilizer.
Stability Label (Nucleosome-Stability Prediction Label)	Predicted label by using a probability threshold of 0.5. Stabilizer indicates the TF binding increases the nucleosome stability, while destabilizer indicates the TF binding reduces the nucleosome stability.

Label Examples

End: Yes

DNA end-binding properties

Groove: Major

Major groove DNA binding

Periodic: Yes

Periodic chromatin regulation

Stability: Destabilizer

Nucleosome destabilizing activity

TF-nucleosome Interaction Help Documentation