DAVID (Functional Annotation Tool) Tutorial

David is the database for annotation visualization and integrated discovery it is most widely used for gene annotation enrichment analysis which stems from gene ontology gene ontology is an effort to maintain and develop a controlled vocabulary of gene and gene product attributes in order to provide consistent annotations and tools for easy access and functional analysis one application of david is to assess the function of a set of differentially expressed genes this list of genes could come from a microarray experiment for example each individual gene in the list may not be statistically significant or the list may consist of many different genes and you're not sure if they're related tools like David gave some insight into whether these genes are part of a specific pathway functionally related or have some other unifying biological theme as an example let's say that you've analyzed the mutation frequencies in glioblastoma and normal brain samples in humans and you've generated this list of 29 most frequently mutated genes you want to know whether these genes are involved in other cancers other diseases or part of the same pathway in other words you're interested in functional annotation which is one of the tools that David offers first you want to go to the david website the menu on the left side shows some of the tools that david offers we're most interested in functional annotation so click on that here you'll see some simple instructions to upload your gene list I find that simply copy pasting control-v my list of 29 genes is a simplest but let's say you had a lot of genes you could also use this upload functionality to submit a file which David will then parse then you need to select the identifier for your list of genes this is just the format of the gene of the data that you're inputting in my case I'll select official gene symbol but David is compatible with many types of input which is definitely an advantage of this resource also if you're not sure about the identifier you can simply select not sure down here and David will match your input against its database to search for an identifier it might also convert your input to its own David ID finally you want to specify the list you're submitting is gene list or background and then you're ready to submit after submitting David might give you some warnings about your input for example here it's found that multiple species have been detected in my gene list this is totally fine because as we see here all 29 genes are in Homo sapiens which is the species that were interested in you can limit annotations to just the species and select the list that you've uploaded the list manager here is useful if you ever find yourself needing to analyze multiple lists the annotation summary results are conveniently displayed on the right you can always check what gene lists and species were used to generate this summary as for these other attributes david has some preset defaults which are shown in the red you can customize these however you wish and when you're satisfied with the settings you can look at three different types of output first the functional annotation clustering shows you different clusters that your genes fall into ranked by enrichment score each cluster contains specific pathways terms or keywords and you can see how many of your genes fall into that category zation and whether it is statistically significant especially after correction for multiple hypothesis testing it also tells you related terms for each entry second the functional annotation chart shows pretty much the same information but without the clustering this might be useful if you're not interesting and interested in overarching biological mechanisms and functions but instead want to look at a specific pathway for example and as an aside if you remember our original question and gene list it's no surprise that most of the top hits here have to do with mutations cancer in general or specific type of cancer finally the function and functional annotation table looks at each submitted genes and returns the many pathways or functions that it might be involved in one thing to note here is that since there are multiple David IDs for each gene there may be some redundancy in general I find the functional annotation clustering to be the most useful output from David but as you can hopefully appreciate from this brief tutorial david is a relatively simple and easy to use tool that helps researchers understand the biological meaning behind a large list of genes or proteins given that we're currently living in the world of big data questions like this one are non trivial David is the convenient and bug free solution and over 21,000 citations further show that it is one of the best in the field of high-throughput functional annotation bioinformatics

Channel: Melinda Song

Views: 17,506

Rating: 4.8032789 out of 5

Keywords: david, bioinformatics, gene ontology

Id: cRYFQADf_vg

Length: 5min 21sec (321 seconds)

Published: Wed May 04 2016