Question: Pathview IDs conversion
0
gravatar for friasoler
2.1 years ago by
friasoler20
Germany
friasoler20 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
myposts • 1.3k views
ADD COMMENTlink modified 2.1 years ago by Manuel Landesfeind1.1k • written 2.1 years ago by friasoler20
2
gravatar for Elisabeth Gasteiger
2.1 years ago by
Geneva
Elisabeth Gasteiger1.2k wrote:

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

ADD COMMENTlink written 2.1 years ago by Elisabeth Gasteiger1.2k

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 REPLYlink modified 2.1 years ago • written 2.1 years ago by Neilfws47k

@Neilfws

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

ADD REPLYlink written 2.1 years ago by Elisabeth Gasteiger1.2k

"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 REPLYlink written 2.1 years ago by Neilfws47k

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

ADD REPLYlink written 2.1 years ago by Elisabeth Gasteiger1.2k
1
gravatar for Manuel Landesfeind
2.1 years ago by
Freiburg, Germany
Manuel Landesfeind1.1k 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 COMMENTlink modified 2.1 years ago • written 2.1 years ago by Manuel Landesfeind1.1k
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