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genescf / GeneSCF

Gene Set Clustering based on Functional annotation
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About the database #12

Closed FYanar closed 3 years ago

FYanar commented 3 years ago

There is something I don't understand. I see that there are 362 genes in geneontology with the number GO:0006936. but the data downloaded with genescf has a total of 104 genes. I guess only direct annotation data is downloaded. I'm wondering is how can I download all data from Gene ontology "without direct annotation". Or why should I use this data in this way?

GO0006936

genescf commented 3 years ago

Hi,

You have already contacted us on Twitter and we explained it to you. And yes, GeneSCF only uses direct annotation. Looks like you need more technical details about gene ontology database. You can get more information about the annotations on, http://geneontology.org/docs/go-annotations/

You can also have a look at these article1 and article2 for better understanding of how GO term and gene association works.

GeneSCF always suggests to use the direct annotations for gene ontology to avoid burden for the statistical inference of your results.

Hope this information helps. Let us know if you need any help regarding GeneSCF.