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Post by DAVID user on Jul 16, 2020 10:18:07 GMT -5
Hello, I'm having some trouble with understanding the functional annotation chart. My gene list is: NM_001181121 NM_001182235 Identifier: REFSEQ_MRNA List type: Gene List Submitting these to DAVID, gives the following output screen (attached below) The part that I'm having trouble with is what exactly the "50%"/"100%", "1"/"2" are referring to. I had thought it was referring to the proportion and number, respectively, of genes in my gene list that are in each gene ontology. However, when I click Chart, on GOTERM_BP_1 for instance, the screen tells me that there are "0 chart records" as "2 gene(s) from your list are not in the output". Any clarification re this would be greatly appreciated, thank you!  |
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Post by DAVID user on Jul 16, 2020 13:10:37 GMT -5
Hello, Your screenshot is a summary of the annotation mapped to the genes in your list per annotation category. For instance, there is GO biological process (GOTERM_BP) annotation associated with one of your genes and GO cellular component (GOTERM_CC) annotation associated with both of your genes. By default, the chart is filtered for terms that have at least 2 genes mapped to it with an EASE Score (modified Fisher Exact) threshold of 0.1. You will therefore get no results for the GO_BP and GO_MF categories due to the count threshold and most likely no results for the GO_CC categories since enrichment of a term from a 2 gene list is not likely. To see all results for the chart report, drop the count and EASE thresholds to 1 and click the "Rerun using options" button as highlighted in the below screenshot.  |
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Post by DAVID user on Jul 16, 2020 13:20:01 GMT -5
Ah yes I see now, thank you for your help with this.
Anna
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Post by GCB on Nov 21, 2020 19:34:42 GMT -5
Hello,
I am having issues understanding UP_KEYWORDS in Functional Annotation Chart. What does that mean?
Thank you.
Basu
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Post by Brad on Nov 30, 2020 9:09:23 GMT -5
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