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geneontology / panther-enrichment

One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
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Improve the usability of PANTHER #11

Open RLovering opened 5 years ago

RLovering commented 5 years ago

Hi I am still not promoting the use of PANTHER in workshops and people asking me for advice. The reason for this is that it is very important to see the list of gene products, either as IDs or gene symbols associated with each enriched GO term. For example on Thursday I was helping someone at UCL and the enrichment.

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Using VLAD we could clearly see that the neutrophil degranulation enriched term had the same enriched genes associated with it as the regulated exocytosis term. this is not surprising in this case because neutrophil degranulation is a child of regulated exocytosis.

screenshot 2019-03-02 at 09 44 26 screenshot 2019-03-02 at 09 44 11

However, it is useful information which can help with understanding the data. plus there are times when it is apparent that the same gps are contributing to almost all of the enriched terms. I realise that these list of gps can be seen by clicking on each individual number next to the GO term, but when 1000 GO terms are often enriched this is not practical. I had hoped that the exported file would have this information, but this is not the case.

please note how useful it is for users to see the ontology and enrichment as displayed in VLAD

PS: please could you include a 'reset' button so that people can clear the enrichment field if they paste the wrong list/text.

Thanks

Ruth

ValWood commented 5 years ago

Same here. For pombe the results are very sub-optimal because panther enrichment doesn't follow the "regulates" relationship. the pathways in this ticket are a nice illustration. All of our users would expect these pathways to enrich to cytokinesis. https://user-images.githubusercontent.com/7359272/53398657-10273180-39a2-11e9-946c-ff5281480953.jpg They are annotated to "regulation of site selection" (or equivalent)

huaiyumi commented 5 years ago

Noted. We will see how to improve the export function to include the list of gps associated to the GO term. For the reset button, do you mean on the Enter ID section on the home page?