Using DAVID for Functional Enrichment Analysis in a Set of Genes (Part 1)

Researchers generate lists of genes through experiments like microarray, next generation sequencing, etc. DAVID is a popular, open source, tool used to explore the functinal enrichment in the gene sets.​

[@DerekBumblesod]

Incredibly helpful, thank you.

[@dpchand]

loved the demo...

[@michellejohnson7918]

Very helpful.... Thank You!

[@vinakanwal8040]

thank u for upload

[@mithilgaikwad4674]

Thank you very much it is really very useful

[@elaheheskandari4546]

Thank you, it was very peractical

[@kocharkhasro387]

Thank you so much

[@veeranagoudayaligar]

Thank you

[@smarwaha6]

Thanks for the demo. Can I use a small list of genes (20-30 genes). I want to cluster them based on their ontology or function. Would "gene functional classification" be a better tool for this?

[@zhuyunhua]

I think so. In this case p-value is not useful.

[@ayachi8521]

Is there any experiment of molecular mechanisms by which increases in levels of microRNA-21 in ovarian cancer may drive drug resistance?

[@CY1RG]

For select species use the background tab to change it

[@potterbond007]

How do you get the GO:ID?

[@NikhilRatna]

Hi, 1) Do you take up regulated and down regulated genes in the same list or separate. Is the analysis/algorithm sensitive to the direction of change. 2) Do you compulsorily set the background list of all the genes identified or all the genes identified and statistically significant then add the list of dysregulated genes?

[@zhuyunhua]

1) What David does to tell you the enrichment in your list of genes. You have to define the list base on what you want to find out. 2) It seems to me that the David doesn't allow you to input a background list, if you are using gene symbols (because that that gene symbols are ambigious by their nature, means not all genes has a gene symbol, and some symbols are redundant). I think in this case they are using all genes as background. But if you have other gene IDs (such as ensembl, or entrez) they may allow you to have a specified background, I haven't tried that.

[@vahidraeesi2801]

Thank you for your helpful video Why DAVID does not recognize a lot of my genes? what i must do? It's transforming options are not helpful

[@zhuyunhua]

several things can contribute to this, 1) the type of ID may be selected wrongly. 2) the organism may be selected wrongly. 3) depends on the reference you use, for instance in RNA-seq analysis, many of the novel gene (newly added to the known genes) can show up in differentially expressed genes, they have a ID but don't have an annotation, so David doesn't recognize them.

[@miakiocean]

hello, i have some question about GO result. I use the same gene list to analysis GO (BP) by Gene Ontology Consortium and david. why it has the different result?

[@burkesquires]

I think the difference is that DAVID checks all three Gene Ontology categories, Biological Process (BP), Molecular function (MF), and Cellular component (CC) at the same time. When I try an analysis at the Gene Ontology site I am asked to run agains only one category at a time. Please also make sure you are using the same host.

[@mailchippull]

Thanks heaps for the tutorial. I have used ensemble gtf files for annotations and my Differential gene expression results are in ensemble gene-ID and ensemble gene-name formats. (example: ENSGALG00000043064 , ENSGALG00000004028). However, when I past my gene IDs, select identifier as 'Ensemble-gene ID', I get the following result in DAVID. "You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your chosen identifier type. Please use the Gene Conversion Tool to determine the identifier type". Hence, I am unable to proceed with the analsyis. Would you please be able to help? Many thanks,G

[@NIAIDBioinformatics]

You can use the Conversion tool from DAVID (david.ncifcrf.gov/conversion.jsp) to correct the issue. Place the list of genes in the box or upload the file. Select the identifier as ensembl and your desired output identifier (should be able to select ensembl as the output as well). After, DAVID usually recognizes the IDs. Hope that helps!

[@mailchippull]

@@NIAIDBioinformatics thank you very much

[@firatkurt4289]

What if you don't know what your Gene ID (refseq, enterez.. etc) ?

[@zhuyunhua]

I think the most helpful friend will be google in this case, see this discussion: www.biostars.org/p/99142/ as biologist, the most common ID we usually have is "official_gene_symbls".

[@limahazarika422]

It was very Helpful. Thank you. But, Whenever I put my gene List, it does not show the Table having count or p-value. I dont understand what went wrong! Kindly Help

[@zhuyunhua]

Because there are multiple steps in between, I don't know exactly what went wrong. But when I tried this morning, it seemed that the website was a little slow. So it take about 1 minute to get me to the next step. For the expected steps, as the video illustrated, you should go through these steps to see the p-values and enriched pathway/GO terms. past gene list (assuming they are gene symbols) --> indicate it is a gene list -->indicate what in your gene list are "official gene symbols" --> click submit --> wait until you see the next step that allow you to choose organism --> click the organism "homo sapiens" (or other organism)--> select organism -->choose one category on the right side of the window that have enrichment result (GO_Term_BP_direct, etc) --> click "chart", it will direct you to the result page where you will see the terms and p-values. Hope this is helpful.

[@NIAIDBioinformatics]

Thank you @Zhu36! I'd also like to offer the DAVID user community as a resource for specific questions groups.google.com/forum/#!forum/daviduserforum

[@jd.clickd]

How to integrate DAVID in asp.net website

[@vandanasuresh9398]

How to get gene list

[@dianaveselu7755]

How can I download the list and use it in excel? all I get is this awful text file. Thanks.

[@senpaislave6898]

watcing this in 2020 and 2020 is the worst year

[@sirazulhaque6773]

SFRH