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Pathview IDs conversion

Hello!

  1. I'm trying to implement "pathview", a very good tool for visualization of metabolic pathway from a list of genes using KEGG, but they require ENTREZ IDs and my list of genes have Uniprot IDs. Does someone knows any way to convert my IDs?
  2. any recommendation how to convert also uniprot IDs to KEGG IDs.......?

Thanks thanks in advance !!!!!

Roberto

References:

  • Luo, W. (2013). Pathview : pathway based data integration and visualization, (Figure 3), 1-16. doi:10.1093/bioinformatics/btt285.2.
  • Luo, W. (2013). Gene set and data preparation
kegg
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updated by Ram Ram • written by friasoler • friasoler

2 answers

You can try the UniProt ID mapping tool: http://www.uniprot.org/uploadlists

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written by Elisabeth Gasteiger Elisabeth Gasteiger

I frequently have issues with this tool and would suggest that using BioMart is the better option. For KEGG ID conversion, there is also the TogoWS REST service.

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written by Neilfws Neilfws

@Neilfws

Please feel free to contact the UniProt helpdesk reporting your issues!

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written by Elisabeth Gasteiger Elisabeth Gasteiger

"Issues" may be the wrong word. It's not that the tool does not work as expected, rather that it sometimes does not do what I want. For example certain conversions, such as HGNC ID to UniProt accession, simply do not return any results, whereas results are returned using BioMart.

It's a useful tool but I would say that it's worth knowing about several conversion tools (UniProt mapper, BioMart, TogoWS, others...) since one may work in cases where others do not.

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written by Neilfws Neilfws

Thanks for the follow-up. Next time you are observing this, please do drop us a note, it's always worth investigating!

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written by Elisabeth Gasteiger Elisabeth Gasteiger

For Gene ID conversion, also have a look at http://www.biomart.org

Further, I think the topic of the question is not suitable because this question refers to Gene-ID convertion which has only limited relation to Pathview software, I think. Probably, you can rephrase the question so others might have it easier to find it.

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written by Manuel Landesfeind Manuel Landesfeind

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