Question: Taking out transcription factors from a tomato transcriptome
0
gravatar for kevluv93
3.1 years ago by
kevluv93150
United States
kevluv93150 wrote:

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?

Thank you!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by kevluv93150

see if you could find overrepresented TF binding motifs in promoter sequences in your genes by promoter analysis tools

 

ADD REPLYlink written 3.1 years ago by F3.1k
0
gravatar for kevluv93
3.1 years ago by
kevluv93150
United States
kevluv93150 wrote:

I actually found what I was looking for. If you need a database of transcription factors and their sequences for Solanum Lycopersicum,  there is a database from Cornell that has this info:

http://bioinfo.bti.cornell.edu/cgi-bin/itak/db_browse.cgi

ADD COMMENTlink written 3.1 years ago by kevluv93150

ok but you asked about the transcription factor in your list....now how you are going to know which of your differentially expressed genes are a transcription factor considering the linked you pasted above...let me know please if possible

thank you

ADD REPLYlink written 3.1 years ago by F3.1k

I think I wrote the question improperly. I have a list of gene IDs that represent my differentially expressed genes. It's not a list of sequences. I meant to say that I wanted to find which genes made transcription factors. Not which areas on my sequences take promoters.

I'm sorry about that, I'll be more careful in the wording of my question

ADD REPLYlink written 3.1 years ago by kevluv93150

actually i should say that i understood your mean improperly and you described your question properly...anyway now you want to compare your list with the list of transcription factor existed in above link?

ADD REPLYlink written 3.1 years ago by F3.1k
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