Dear specialists of bioinformatics,
I would like to identify candidate genes directly regulated by a transcription factor (TF) from the list of differentially expressed genes (DEGs) of a TF-Knockout (KO) mutant without using ChIP-seq data.
What I did; To find downstream targets of TF-A (a gene of interest) of tomato, I made a knockout line of TF-A gene and conducted RNA-seq using total RNA sample from fruit.
Then, I obtained several hundreds of DEGs (Up and Down) by comparing a RNA-seq data of wild type and the TF-A-KO line.
What I can do now; I know the canonical binding motifs of TF-A. To identify the direct targets* of TF-A from the DEGs, of course, I can check the presence of TF-A binding motifs in the promoter region of all DEGs one by one. But, it's very time-consuming.
*direct target; here, it means the gene that TF-A binds to the promoter region and modulate its mRNA expression.
What I want to know; Are there any web tools or programs to identify the DEGs which have the specific TF-binding site in their upstream region (like 2kb from TSS) from the DEGs list ? What kind of approach can I take except the one-by-one method mentioned above ?
I'm using a mac, I have few experience of programming. I just started studying the basic of R.
Thank you for sharing your knowledge