I have a list of differentially expressed genes from an experiment where we compared the transcriptome of two different Solanum lycopersicum plants. I want to take out all of the transcription factors from this list of differentially expressed genes.
Right now the only method I've been trying is sorting the genes into GO terms and taking out all the genes under GO categories such as "transcription factor". I'm also manually going through the list of differentially expressed genes and using the literature to see what other transcription factors are in my list of genes that the gene ontology didn't get.
I feel like this is an inefficient and wrong way of doing this. Is anyone aware of a database or some methods to search for transcription factors in a list of differentially expressed genes from a tomato transcriptome? I don't want to re-invent the wheel, when you have to extract genes with certain functions from a big list of genes how do you do it?