Question

Questions about DAVID

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8.3 years ago

hxlei613 ▴ 100

I have been using DAVID to analyze a gene list recently.

What I'm confused about is Functional annotation clustering. After uploading a gene list, selecting Functional annotation clustering, I get Annotation Summary Results. There are GOTERM_BP_1, GOTERM_BP_2, GOTERM_BP_3, GOTERM_BP_4, GOTERM_BP_5, GOTERM_BP_ALL, GOTERM_BP_FAT and so on under Gene_Ontology.

So here is the question, what does 1,2,3,4,5,ALL and FAT mean? I can't find any explanation.

Thank you very much!

DAVID • 15k views

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.3 years ago by hxlei613 ▴ 100

Ram · Answer 1 · 2016-01-08

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8.3 years ago

vivekbhr ▴ 690

BP_1 to BP_5 are the levels of GO terms with increasing specificity (1 is least,5 is most). BP_ALL is all of the levels combined..
GO FAT filters out very broad GO terms based on a measured specificity of each term, so it's like filtered BP_ALL..

So you can use whatever category suits your needs.. More specific ones will have less genes in each category, as expected.

ADD COMMENT • link updated 4.3 years ago by Ram 43k • written 8.3 years ago by vivekbhr ▴ 690

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Thank you very much!

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 8.3 years ago by hxlei613 ▴ 100

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how to draw a pie chart for molecular,cellular,biological processes from the DAVID output

ADD REPLY • link 7.6 years ago by rajasekargutha ▴ 60

score 2 · Answer 2 · 2017-10-24

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6.5 years ago

moldach ▴ 130

As of October 2016 there has been a new GO category added (GO Direct), which provides GO mappings directly annotated by the source database (no parent terms included). I'm not sure why DAVID selects this as the default but it has very low specificity.