Non-specific annotations in KEGG, Pfam for plant denovo RNA seq data
While analysing plant de novo transcriptome data, I have come across non-specific annotations from Pfam and KEGG pathway annotations. These are not intended in the data set. Has anybody come across similar issues while doing de novo RNA seq data analysis? How to get rid of these annotations?
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Can you give us some context for these
non-specific annotations?Yes, I have plant RNA seq data and I got KO annotations like, Bacterial secretion system, Viral life cycle - HIV-1, Fanconi anemia pathway, p53 signaling pathway, Cardiac muscle contraction etc. Also, some Pfam annotations like, Bac_luciferase, BRCT, Agenet, Voltage_CLC and so on. No clue how to deal with this.
Those are, even nowadays, still very common when doing plant research. Not much you can do about it.
I also don't see any immediate need to get rid of these. Why do you feel you need to remove them?
will that not interfere with my data analysis? like if I want to report the highly represented pathways in any particular sample then these kinds of non-specific entries are problem. also, while reporting the transcriptome, will this not creat any issues? Does people normally report de novo RNA seq data this way?
OK, the 'annotations' you list above are indeed quite exotic for a plant sample (I posted before you added that info). I , wrongly apparently, assumed you were talking about things like 'transcription' or other general , non-specific terms initially
Are you sure you have a clean sample? It sounds like it might be contaminated. It might pay off to first do some analyses on that aspect to assure the data is fine.
Ok! Thank you for your comment. It would be really great if you can suggest a tool (if any) for filtering out such hits.
If you only have a few transcripts with these 'unusual' annotation terms, you can use BLASTx to check whether the top hit matches your target organism. However, keep in mind that you may be dealing with proteins that have a broad taxonomic distribution. Here are a few examples::
Proteins with a Voltage_CLC domain are also found in plants: https://www.ncbi.nlm.nih.gov/protein/?term=(Voltage_CLC)+AND+%22green+plants%22%5Bporgn%3A__txid33090%5D
Arabidopsis has several proteins annotated in KEGG as part of the Viral life cycle - HIV-1: https://www.kegg.jp/pathway/ath03250