Functional enrichment and visualization of metatranscriptomics data
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10 weeks ago
shail.nair05 ▴ 20

Hi, I am new to clusterProfiler. Is it possible to use clusterProfiler for metatranscriptomics DEG data (deseq2)? As i read from http://yulab-smu.top/clusterProfiler-book/chapter3.html#input-data for unsupported organisms, one need to create TERM2GENE and TERM2NAME file, which according to the guide requires a organism specfic gmt file.

My sample is of mixed bacterial transcript expression (metatranscriptomics). I ran deseq2 and wanted to do functional gene enrichment analysis.

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TERM2NAME is optional. TERM2GENE is a data.frame with first column of term ID (wpid)and second column of corresponding mapped gene:

  wpid  gene
1 WP23  4690
2 WP23  5781
3 WP23 11184
4 WP23  6195
5 WP23  4609
6 WP23   998

In the example above the term ID correspond to the wikipathway IDs but can be any annotation term (e.g. Gene Ontology ID). For metagenomic/metatranscriptomic data you can use eggNOG to annotate your transcripts with GO

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Thanks. is it possible to use kegg for metagenomic/metatranscriptomic?

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Yes, you can use KEGG pathways id instead of GO. eggNOG will also annotate your transcripts with the KEGG annotation terms.

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will try with kegg. Thanks :)

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