Questions tagged [conversion]

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2answers
80 views

What is the best way to programmatically convert Ensembl ids from one release to other? e.g. transcript ids from release 75 to 100

3 solutions that I had to unfortunately rule out. Potential solution #1 As far as I know, the conventional way is to do this is by using CCDS ids (e.g. using biomart). However, the issue is that, as I ...
0
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1answer
19 views

how to get FlyBase ID conversion table

FlyBase uses systematic naming of genes, transcripts and proteins in a format FBtypeNUMBER. However, the numbers are not the same for genes and their products. For ...
1
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3answers
2k views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
6
votes
2answers
8k views

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart. I tried to get a kind of conversion table for all human genes. ...
3
votes
1answer
841 views

Missing data mappings in mygene.info while trying to convert Genes Ensembl Ids to Entrez Ids

I need to convert a lot of Ensembl Ids to the relative counterpart in Entrez (e.g., ENSG00000157764 > 673). I found mygene.info ...
4
votes
2answers
264 views

Convert Reactome Protein IDs to Pathway IDs?

I have a list of about 50k 'Protein IDs' from Reactome. Is there a simple way to get all the corresponding 'Pathway IDs' for each protein? What is the best service to use? (I'm guessing I can use the ...
6
votes
1answer
853 views

Entrez or Ensembl gene IDs?

I'm using several datasets that are encoded using either Entrez or Ensembl IDs to specify genes, and need to decide on which to standardise on. Are there any major reasons to use one over the other? ...
12
votes
6answers
1k views

Converting gene names from one public database format to another

This is a question from /u/apivan19 on reddit. The original post can be found here. I have some proteomics data that was given to me with the UniProt gene identifiers in column 1. I've been trying to ...