# TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila

## TL;DR

TF2TG is a new online tool that helps identify which genes are regulated by specific transcription factors in fruit flies by combining various biological data.

## Contribution

TF2TG integrates in vitro and in vivo data with protein interactions and chromatin accessibility to predict transcription factor targets in Drosophila.

## Key findings

- TF2TG combines TF binding motifs, protein interactions, transcriptomics, and chromatin data to identify gene targets.
- The tool ranks candidate genes and identifies condition-specific TF binding in Drosophila.
- Only a subset of potential TF binding sites are functionally relevant due to synergistic interactions.

## Abstract

Sequence-specific transcription factors (TFs) are key regulators of many biological processes, controlling the expression of their target genes (TGs) through binding to the cis-regulatory regions such as promoters and enhancers. Each TF has unique DNA binding site motifs, and large-scale experiments have been conducted to characterize TF–DNA binding preferences. However, no comprehensive resource currently integrates these datasets for Drosophila. To address this need, we developed TF2TG (“transcription factor” to “target gene”), a comprehensive resource that combines both in vitro and in vivo datasets to link TFs to their TGs based on TF–DNA binding preferences along with the protein–protein interaction data, tissue-specific transcriptomic data, and chromatin accessibility data. Although the genome offers numerous potential binding sites for each TF, only a subset is actually bound in vivo, and of these, only a fraction is functionally relevant. For instance, some TFs bind to their specific sites due to synergistic interactions with other factors nearby. This integration provides users with a comprehensive list of potential candidates as well as aids users in ranking candidate genes and determining condition-specific TF binding for studying transcriptional regulation in Drosophila.