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Questions about DAVID

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
• 18,170 views • link
updated by Ram Ram • written by hxlei613 hxlei613

2 answers

  • 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.

• 0 views • link
updated by Ram Ram • written by vivekbhr vivekbhr

Thank you very much!

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updated by Ram Ram • written by hxlei613 hxlei613

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

• 1 views • link
written by rajasekargutha • rajasekargutha

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.

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written by moldach moldach

Which one is best suggested to annotate a set of up-regulated ges?

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written by Arindam Ghosh Arindam Ghosh

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