Enrichment from AmiGO2 to Panther

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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Enrichment from AmiGO2 to Panther #1

Closed mcourtot closed 7 years ago

mcourtot commented 7 years ago

From a helpdesk query, http://jira.geneontology.org/browse/GO-1405

Issue:

go to http://amigo.geneontology.org/rte and select 'biological process only'
hit submit, request is passed to Panther server, which then says 'Error parsing request, invalid ontology type specified'

Additionally, there doesn't seem to be an option on the Panther website to select manual only annotations.

mcourtot commented 7 years ago

@kltm just clarified that this page shouldn't have been accessible on AmiGO, therefore this 'bug' can be ignored.

However, is there a way to achieve what the user originally wanted, i.e., perform an enrichment analysis using only manual annotations? In the original helpdesk ticket they mentioned they couldn't find the option on the Panther site.

mcourtot commented 7 years ago

Anushya added that Panther doesn't support manual annotations anymore. Closing this ticket.