Plant-DTI predicting interactions of DNA-binding domain and TFBS in plants

Prediction Tool

Enter your input sequence

Transcription factor or DNA-binding domain sequence

Correct DNA-binding domain sequence is required.

Use a Example sequence | Clear sequence

Promoter sequence

DNA sequence at least 7 bp is required, ambigous base not allowed.

Use a Example sequence | Clear sequence

Set your parameter

Interaction probability threshold 0.7

Definition

DNA-binding domain (DBD) is a structural motif region in a transcription factor that recognizes a specific DNA sequence.

The model covers 26 DBD types of 30 TF families read more

The promoter sequence is an upstream sequence from the transcription start sites of a gene which proteins can bind and initiate gene transcription.

The promoter region contains specific DNA sequences for DNA-binding proteins; transcription factor (TF), called transcription factor binding site (TFBS).

A sequence length promoter should be ≥ 7 bps. An ambiguous base is not allowed.

For a setting criterion for predicting interaction between DBD and TFBS, the interaction probability should be greater than 0.5. The default threshold was set at 0.7.

The higher probability threshold is the higher confidence of the predicted interaction.

Prediction Results

DNA-binding domain sequence

Transcription factor binding sites on promoter sequence

Table result of PlantDTI prediction

Export CSV

Description of terminology

DNA-binding domain sequence

Amino acid sequences of DNA-binding domain in a TF protein. It was highlighted in red and shown its DBD type based on Pfam identification.

Transcription factor binding sites on promoter sequence

DNA sequences of a promoter region of an interested gene. The predicted TF binding sites on both strands (+ strand and - strand) were highlighted in blue.

Table result of interaction prediction

The predicted interaction results were shown in table format. User can sort and filter the result based on any keywords in the column e.g., prediction score equal to 1 for obtaining the highest confident predicted interactions. User can download the table result in csv format. The meaning of each column result is described below.

TF binding site

Predicted TF binding site on the queried promoter sequence.

Length

Predicted TF binding site sequence length.

Start

The start position of predicted TF binding site, the reported result relied on position of positive strand used as input sequence.

End

The end position of predicted TF binding site, the reported result relied on position of positive strand used as input sequence.

Strand

Strand of DNA which TF binding site is located.

Model type

Method to generate negative data for Plant-DTI tool which can be either random DBD-TFBS pairs (RP) or random nucleotide within TFBS sequence (RW).

Prediction score

The interaction probability predicted via Plant-DTI for each queried pair between DBD and TFBS.

Citation

Ruengsrichaiya B, Nukoolkit C, Kalapanulak S and Saithong T (2022) Plant-DTI: Extending the landscape of TF protein and DNA interaction in plants by a machine learning-based approach. Front. Plant Sci. 13:970018. doi: 10.3389/fpls.2022.970018