Plant: https://planttfdb.gao-lab.org/

Animal: https://guolab.wchscu.cn/AnimalTFDB4//#/

Steps:

1. Download the sequences, and make a local database

2. Get the protein sequences of your gene list

3. Blast your sequences as query against the database (set alignment threshold and e value cutoff accordingly)

4. Select tabular format as your output file, so that it would be easier to sort your data in excel

Hi Muhammad,

The relationship between a transcription factor and its target gene can also be determined by reviewing the literature. The Alphafoldserver website can be used to analyze the interaction between transcription factors and target genes.

First, access the Alphafoldserver website and select two modes:

• Protein: Corresponding to the transcription factor sequence (can be retrieved from the UniProt database; species information should be noted).
• DNA: Corresponding to the target gene sequence (can be found in the NCBI database), typically selecting the first 2000 bases of the gene for analysis.

After submission, the results will display the binding affinity between the transcription factor and the target gene.

Hope this helpful, Feel free to reach out for more details.

I suggest these tools:

1. ENCODE: Provides experimentally validated TF binding sites from ChIP-seq experiments for a wide range of TFs and cell types.

2. TRRUST: A manually curated database of TF-gene regulatory interactions supported by experimental evidence (e.g., ChIP-seq, reporter assays).

3. ChIP-Atlas: Integrates ChIP-seq data from public repositories (e.g., ENCODE, GEO) to identify TFs binding to specific genes or genomic regions.

I hope this helps.