Genes from my list are not in the output

Florencia Mascardi
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Genes from my list are not in the output Aug 3, 2021 17:44:57 GMT -5

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Post by Florencia Mascardi on Aug 3, 2021 17:44:57 GMT -5

Hello! I would really appreciate your help with this issue.

I have submitted a list of 1808 genes identified by official gene symbol. 1600 out of them have been recognized by DAVID's database.
I am interested on the Gene Ontology related terms, and 88,7% (1419) of my genes got matched to a GO-BP term. I click on "Chart" but then only 229 chart records are shown, and at the bottom of this list it says "802 genes from your list are not in the output". So I'm missing over 50% of the genes here.

What is happening here? Is there some way I can solve this? I've already tried changing the threshold "Count" to 1, but nothing changed.

Thank you in advance for your response, and sorry if my English is not very good (my first language is Spanish).

Florencia Mascardi Guest	Genes from my list are not in the output Aug 3, 2021 20:40:05 GMT -5 Quote Select Post Deselect Post Link to Post Back to Top Post by Florencia Mascardi on Aug 3, 2021 20:40:05 GMT -5 Solved! Sorry for bothering you

Donald Guest	Genes from my list are not in the output Nov 10, 2022 4:13:00 GMT -5 Quote Select Post Deselect Post Link to Post Back to Top Post by Donald on Nov 10, 2022 4:13:00 GMT -5 Hello Florencia, Please how did you solve it? I am having the same problem Thank you

B@N@2C2
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Genes from my list are not in the output Sept 3, 2023 8:50:59 GMT -5

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Post by B@N@2C2 on Sept 3, 2023 8:50:59 GMT -5

The number of genes from your list in the output are depends on the thresholds. The default thresholds are count (gene count) = 2 and EASE (Modified Fisher Exact P-value, ranges 0 to 1) = 0.1. To display maximum number of genes shown on the list, set count = 1 and EASE = 1.0

Fiza Guest	Genes from my list are not in the output Sept 4, 2023 4:05:57 GMT -5 Quote Select Post Deselect Post Link to Post Back to Top Post by Fiza on Sept 4, 2023 4:05:57 GMT -5 Hello! I have a small query, Why are not we getting enrichment terms for all the genes we provided as input in the output file? There are always some genes left as xx genes from your list are not in the output. Thank you.

Sven
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Genes from my list are not in the output Dec 29, 2023 13:34:02 GMT -5

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Post by Sven on Dec 29, 2023 13:34:02 GMT -5

Hi,

I am adding to this thread because I still do not understand why some of my input genes are missing in the output.

FYI: My input gene list consists of 329 Pseudomonas aeruginosa (PAO1) genes of which DAVID recognizes 326 in the PAO1 genomic background list.
When I run the functional annotation chart tool, the results show that 101 genes are not contained in the output. Even if I set both "Count" and "EASE" to "1".

It is said in the FAQs that genes can be missing in the output if they are incompletely annotated (no functional summary text or no GO classification.
However, for some of the genes in question I can find GO classifications online (not sure what is meant by functional summary text).

Any idea why these genes are still excluded from the annotation chart?

DAVID Bioinformatics

Genes from my list are not in the output

Post by Florencia Mascardi on Aug 3, 2021 17:44:57 GMT -5

Post by Florencia Mascardi on Aug 3, 2021 20:40:05 GMT -5

Post by Donald on Nov 10, 2022 4:13:00 GMT -5

Post by B@N@2C2 on Sept 3, 2023 8:50:59 GMT -5

Post by Fiza on Sept 4, 2023 4:05:57 GMT -5

Post by Sven on Dec 29, 2023 13:34:02 GMT -5

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