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Nov 28 '18 at 14:45 history edited Emily_Ensembl CC BY-SA 4.0
added 9 characters in body
Nov 8 '18 at 11:55 history edited Emily_Ensembl CC BY-SA 4.0
added 1569 characters in body
Nov 8 '18 at 11:44 comment added Emily_Ensembl Yes, that's it. But change the attributes to whatever you want to see in your results table.
Nov 8 '18 at 11:40 comment added gabt ops! sorry Llopis and Emily, you're right. This should work bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/….
Nov 8 '18 at 11:20 comment added llrs @gabrielet the first section of your link (127.0.0.1:19280) is for a local port of your machine! We can't access your machine, so we cannot see the code you are mentioning
Nov 8 '18 at 11:18 comment added gabt Emily, if you click on it then it does not work, if you copy-paste in a new tab, definitely it will. Otherwise, from the page that it opens, I'm focusing on the section 4.6 Retrieve all entrezgene identifiers and HUGO gene symbols of genes which have a “MAP kinase activity” GO term associated with it.
Nov 8 '18 at 11:11 comment added llrs @Emily_Ensembl Because in Stackexchange the are for clarifications and improvements of questions and answers, and as such the content is assumed to be added to the relevant question or answer. Also they are considered "second class citizens"...
Nov 8 '18 at 11:10 comment added Emily_Ensembl I don't have permission to connect to that. Can you send it as a proper URL.
Nov 8 '18 at 11:07 comment added gabt Emily, one more detail. The example query you sent, is equivalent to this piece of code (changing the mart and the GO entry)? 127.0.0.1:19280/library/biomaRt/doc/….
Nov 8 '18 at 10:28 comment added Emily_Ensembl Why would the comments be deleted?
Nov 8 '18 at 10:27 comment added llrs @Emily_Ensembl please edit the comments to your answer (the comments might be deleted and there are very useful comments). Thanks for answering this
Nov 8 '18 at 10:25 comment added Emily_Ensembl Here's a BioMart query that gets you exactly what you need in human
Nov 8 '18 at 10:11 comment added Emily_Ensembl No, don't worry about looking in GO. Just put the one term you have into BioMart. It will find all genes associated with your term and all genes associated with its children. A term may have more than one parent term, but if it's associated with a gene then everything about that term is associated with the gene. The term is not associated with the gene via parent X or parent Y, it means that both are relevant. So if the child term is associated with the gene, then the parent term is by proxy.
Nov 8 '18 at 9:33 comment added gabt ok, so as you're suggesting what I should look, in GO, is for the children of my GO term. But a child of my term can contain genes from other parents, isn't it? according to this link geneontology.org/page/ontology-structure it seems that some kind of association may appear between different branches.
Nov 8 '18 at 9:27 history answered Emily_Ensembl CC BY-SA 4.0