Clusterprofiler for KEGG enrichment (non-model species)
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7.1 years ago
sbchua.1990 ▴ 50

Hi, I wish to use clusterProfiler for KEGG pathway enrichment (non-model species, Pleurotus pulmonarius). I want to use my whole transcriptome as background. I now have files for whole transcriptome and DEG in the following format:

TRINITY_identifier KO_number

How can I proceed from here? What kind of extra input files are needed?

gene rna-seq R • 4.2k views
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I am not sure for clusterProfiler in particular, but normally if you want to do KEGG or GO analysis with non-model species, you'll first need to know which genes of your mushroom map to which KEGG pathway or GO term. I don't think TRINITY identifiers are sufficient for this purpose.

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Thanks for reply. Ko_number at second column. Do you have any suggestion for suitable software?

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When I worked with non-model species, a decade ago, I used blast2go software for this. But I am not sure if this is still the best approach nowadays (and if it is still free software). I 've been working for too long with model species now.

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6.8 years ago
sutturka ▴ 190

May be this document will be useful.

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