Pathview IDs conversion

Question: Pathview IDs conversion

5.3 years ago by

Germany

friasoler • 20 wrote:

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

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modified 2.7 years ago by Biostar ♦♦ 20 • written 5.3 years ago by friasoler • 20

5.3 years ago by

Elisabeth Gasteiger • 1.9k

Geneva

Elisabeth Gasteiger • 1.9k wrote:

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

ADD COMMENT • link written 5.3 years ago by Elisabeth Gasteiger • 1.9k

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.

ADD REPLY • link modified 5.3 years ago • written 5.3 years ago by Neilfws ♦ 49k

@Neilfws

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

ADD REPLY • link written 5.2 years ago by Elisabeth Gasteiger • 1.9k

"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.

ADD REPLY • link written 5.2 years ago by Neilfws ♦ 49k

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

ADD REPLY • link written 5.2 years ago by Elisabeth Gasteiger • 1.9k

5.3 years ago by

Manuel Landesfeind • 1.3k

Göttingen, Germany

Manuel Landesfeind • 1.3k wrote:

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.

ADD COMMENT • link modified 5.3 years ago • written 5.3 years ago by Manuel Landesfeind • 1.3k

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