Dear MapMan Team,

Your development on MapMan is very impressive. I am working on Oryza sativa Japonica Group and have ~200 RNA seq experiments which I am trying to analyze.I was wondering is it possible for a user to load own mapping of gene ids to e.g. KEGG to see pathway comparisons/enrichment, etc in MapMan? And is it possible for you to provide/include Refseq version of Oryza sativa japonica group gene ids as provided by NCBI and KEGG?

I note there are many versions of Oryza sativa Japonica Group assemblies, and there are no stable gene ids to work with. To map our RNA seq data, we choose the latest one from NCBI https://www.ncbi.nlm.nih.gov/assembly/GCF_001433935.1/ (call it Refseq version) where gene locus ids corresponds to NCBI's stable gene database ids and KEGG's (31126) annotations e.g. http://www.genome.jp/dbget-bin/get_linkdb?-t+genes+genome:T01015


Example Locus Id: LOC107276001 has
NCBI's geneId 107276001 and it has a corresponding
kegg Id as osa:107276001 in KEGG:http://www.genome.jp/dbget-bin/www_bget?osa:107276001

There are ~7000 genes with assigned KO ID needed to see pathway mappings. In an experiment I took all of 31126 genes from this set and BLASTed against all KEGG genes with defined KO numbers. I am able to increase this mapping to KO numbers from ~7000 to ~20000. It would have been great if I could take these mappings and RNA-Seq expression data into MapMan to study enrichment/pathway analyses, do you have any suggestions?

Best Wishes,

Intikab

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Intikhab Alam, PhD

Research Scientist
Computational Bioscience Research Centre (CBRC), Building #3, Office #4328
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, KSA
W: http://www.kaust.edu.sa