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Is it any database or software to find genes which are involved in one secondary metabolite pathway?

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

rna-seq secondary metabolite pathway genes
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written by hodatn • hodatn

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.

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written by Kevin Blighe Kevin Blighe

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