TSPTFBS 2.0: trans-species prediction of transcription factor binding sites and identification of their core motifs in plants.

ABSTRACT:

Introduction

An emerging approach using promoter tiling deletion via genome editing is beginning to become popular in plants. Identifying the precise positions of core motifs within plant gene promoter is of great demand but they are still largely unknown. We previously developed TSPTFBS of 265 Arabidopsis transcription factor binding sites (TFBSs) prediction models, which now cannot meet the above demand of identifying the core motif.

Methods

Here, we additionally introduced 104 maize and 20 rice TFBS datasets and utilized DenseNet for model construction on a large-scale dataset of a total of 389 plant TFs. More importantly, we combined three biological interpretability methods including DeepLIFT, in-silico tiling deletion, and in-silico mutagenesis to

SUBMITTER: Cheng H 

PROVIDER: S-EPMC10203575 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature