Suggestions for automated functional analysis of transcripts

Question

[bioinformatics_newbie]

Hello,

I am relatively new to bioinformatics and RNA-Seq differential gene expression. I was able to generate a matrix of significantly expressed gene ids from bacteria. I would like to categorize these genes based on cellular function (membrane components, metabolism proteins, cell stress and so on). I have a list of a couple hundred genes that I could look up on NCBI gene, but am thinking there is an easier way.

I tried websites like DAVID but it does not seem to recognize the gene ids. I entered names like PD_RS00325 which NCBI database identifies as a gene in my bacteria of interest. I also tried Blast2Go in Omicsbox, but I seemed to have trouble annotating the list because it was not in the right format. Any suggestions on some way to automate this process of identification of the cell functions of these genes would be very helpful.

Thanks for your time.

[jumagarilla]

Did you select the organism the gene IDs belong to before running the analysis? If I remember correctly, DAVID maps the input IDs to human gene IDs.

[bioinformatics_newbie]

Yes, I added the name of the species after selecting "official_gene_id." DAVID software prompted me to convert the ids to Entrez IDs but mentioned that all my gene ids were uncharacterized. I don't think that is the case since you can search the gene ids and pull up names and nucleotide sequences in NCBI databases.

Answer 1

[EagleEye]

Best command line option to automate any number of gene list and multiple organisms, Gene Set Clustering based on Functional annotation (GeneSCF)

[bioinformatics_newbie]

I checked out the link to the software and it sounds really good! The prerequisites section says that I have to use Linux or Ubuntu but I am using a Mac. It also mentioned using Perl programming language and I don't have that one either because I was using python. I am not sure if it will work. I was wondering if I could try the DAVID software one more time and perhaps I entered the wrong filters to start the software. I could try others if needed.