Question: Is it any database or software to find genes which are involved in one secondary metabolite pathway?
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gravatar for hodatn
3.1 years ago by
hodatn0
hodatn0 wrote:

Hi Biostars,

I have a list of secondary metabolites in a medicinal plant which doesn't have whole genome sequences. I want to find genes which are involved in synthesis of these secondary metabolites pathway. Is it any database or software to find genes which are involved in one secondary metabolite pathway?

(RNA seq data is available)

Thank you

ADD COMMENTlink written 3.1 years ago by hodatn0

Metabolite pathways are still being curated and we are very far from fully understanding these, in human, at least. For example, in any blood sample, upward of 15,000 metabolites can be identified by a mass spectrometer, >90% of which are unidentified / unknown to science. For plants, I am not sure.

If you have a list of metabolites, a very simple tool to use is MetaboAnalyst, hosted at McGill University in Canada: http://www.metaboanalyst.ca/ I think that your metabolites have to be HMDB IDs. MetaboAnalyst has an Integrated Pathway Analysis section that allows you to analyse metabolites and genes together.

Further, if you have RNA-seq data and can derive the FASTA sequences of interest, you could use blastx (https://blast.ncbi.nlm.nih.gov/Blast.cgi) in order to try to identify the transcript's function by searching for proteins of similar sequence.

ADD REPLYlink written 3.1 years ago by Kevin Blighe66k
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