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Questions tagged [gene-ontology]

The Gene Ontology (GO) is a collection of annotations of genes from multiple species to terms describing the functional role of those genes. The terms are organized in a graph structure that allows for propagation of information. See http://geneontology.org

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different results coming from biomart online and biomaRt R library

I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term. So, if I use the webservice as in this query: I get at least 50 genes. If I download the ...
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Retrieve all genes for a specific gene ontology

I'm having a bit of confusion about how can I retrieve all the genes that are associated to a specific gene ontology. Lets say I need to find all the genes that are associated with this GO entry: ...
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NCBI xml-format Printing nodeValues from tags with the same names

I would like to retrieve all Other-source_anchor on the level of DNA binding from within a Gene Ontology XML file using php. If I try this with my code, I only get Gene Ontology back and not the ...
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How can I create my own GO slim?

I know there are existing GO slims predefined. But does anyone know how I can create my own collection of GO terms for enrichment analysis?
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Obtain CD (cluster of differentiation) marker expression information

There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so ...
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Retrieving a list of human genes having GO associations

I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.
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How can I create my own GO association file (gaf)?

This question is based on a question on BioStars posted >2 years ago by user jack. It describes a very frequent problem of generating GO annotations for non-model organisms. While it is based on ...