Quick Start Tutorial for the DAVID Bioinformatics Resources Last Updated February 2022
DAVID Bioinformatics Resources (2021 Update) aboratory of Human Retrovirology and Immunoinformatics (LHRI)
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The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes. These tools are powered by the comprehensive DAVID Knowledgebase built upon the DAVID Gene concept which pulls together multiple sources of functional annotations. For any given gene list, DAVID tools are able to: Identify enriched biological themes, particularly GO terms ☎  Discover enriched functional-related gene groups 🌸 Cluster redundant annotation terms & Visualize genes on BioCarta & KEGG pathway maps ☞ Display related many-genes-to-many-terms on 2-D view. R   Search for other functionally related genes not in the list ☞ List interacting proteins ☞ Explore gene names in batch 🌸 Link gene-disease associations
W  Multiple positions available in LHRI W
The Laboratory of Human Retrovirology and Immunoinformatics (LHRI) has collaborated with the National Institute of Allergy and Infectious Diseases (NIAID) and supported NIAID clinical trials for patients infected with HIV mutants resisting anti-retroviral therapy. LHRI has isolated the multiple-class drug-resistant (MDR) variants from patients and characterized each variant's drug sensitivity and infectivity. The study aims to define salvage therapy and develop novel therapy (chemotherapy and immunotherapy). During the investigation, LHRI has characterized the emergence of novel mutations on drug susceptibility and viral replication. LHRI is a pioneer in researching the anti-viral cytokine, Interleukin-27, DNA- repair protein (Ku70)-mediated innate immune response against HIV and other virus co-infection, and novel subsets of immune cells. LHRI maintains the Database for Annotation, Visualization and Integrated Discovery ( DAVID ). About-DAVID- rmatics Resources (2021 Update). NIAID/NIH First, switch to the Upload tab Tell us how you like the tool Contact us for questions 1. Click on a demo list or paste or upload your gene/protein list "box A" -> Select Identifier as  "Affy_ID" -> List Type as "Gene List" -> Click "Submit" button 2. Select the identifier type corresponding to your list. 2a. If “OFFICIAL_GENE_SYMBOL” is selected, a new parameter will appear allowing you to indicate your species of interest by typing the name or – taxonomy id. 3. Choose your list type. Note: A gene list must be uploaded before a background.
Tell us how you like the tool Contact us for questions Which DAVID tools to use? Choose A DAVID Tool to begin exploring your gene list. Help choosing is available in DAVID and at the end of this tutorial. In the List tab, you will see species listed for your list and a list name.
This tool provides a view containing gene names and taxonomies for a list of identifiers as well as links to more specific annotation for a given gene (Gene Report) and methods for viewing related genes (Related Genes) from the list or background population. This tool provides a quick and informative look at the list before proceeding with more in-depth analyses.  A link is provided to downloaded a tab-delimited file for any tool output in DAVID.
Gene List Report
Help and Manual Current Gene List: demolist2 Current Background: Homo sapiens 372 DAVID IDs
The DAVID Gene Report contains annotations that are more specific to a given gene. The DAVID Gene Report header will contain the user’s original uploaded gene list identifier, the DAVID Gene Name, including the gene symbol, a link to find Related Genes in the user’s list or background gene set, based on shared functional annotation, and the taxonomy.  Links with further information for the gene specific data are also provided when available. A link is provided to downloaded a tab- delimited file for any tool output in DAVID.
The Functional Annotation Summary provides annotation type specific annotation for the user’s list including gene counts and percentages and organizes the annotation types into categories.  From the summary, a user can use the Functional Annotation Table, Functional Annotation Chart or Functional Annotation Clustering tools with one or multiple annotation types.  Default selections are made for quick usage. ❏ General_Annotations (0 selected) ❏ Interactions (1 selected)田Literature (0 selected) ❏ Pathways (3 selected) ❏ Protein_Domains (4 selected 🌸 Tissue_Expression (0 selecte ***Red annotation categories denote DAVID defin Combined View for Selected Annotation Functional Annotation Clustering Functional Annotation Chart Functional Annotation Table
The Functional Annotation Table provides annotations associated with a user’s list of genes for user-selected categories in tabular format.  This tool quickly links the user's list to the breadth of annotation contained in the DAVID Knowledgebase with no statistical inference and is well suited for looking at genes on an individual basis, providing links to more detailed information about the associated annotation. A link is provided to downloaded a tab-delimited file for any tool output in DAVID.
Functional Annotation Table
Help and Manual Current Gene List: demolist2 Current Background: Homo sapiens 372 DAVID IDs
This tool provides enrichment analysis using a modified Fisher Exact Test to identify the most overrepresented annotation terms associated with a user's gene list as compared to a background gene set. Flexible options are provided to change gene count and p-value thresholds and display different aspects of the analysis. Clicking blue bars will provide details of underlying genes, related terms (RT) can be found based on shared user genes and sublists based on genes underlying one or more terms may be created for drill-down analysis.
Functional Annotation Chart
Help and Manual Current Gene List: demolist2 Current Background: Homo sapiens 372 DAVID IDs日Options Count  2 EASE 0.1 Thresholds: ■Bonferroni Fisher Exact Fold Enrichment Rerun Using Options Create Sublist
This tool groups similar annotation terms together using the Kappa statistic to determine pairwise similarity scores and a novel fuzzy clustering algorithm.  The fuzzy feature of the clustering algorithm allows a term to participate in multiple groups.  The tool helps the user focus on biological themes associated with their gene list by reducing redundancy through the grouping of biologically similar terms.  This complements the Functional Annotation Chart as some enriched terms may not be grouped if they do not have enough similarity with other terms.  As with other tools, options are available for power users and defaults set for quick analyses. Help and Manual Current Gene List: demolist2 Current Background: Homo sapiens 372 DAVID IDs
This tool allows a user to group genes which are functionally similar together, thereby providing a biological network view of their list. As with the Functional Annotation Clustering tool, this tool uses a Kappa statistic to measure similarity between pairs of genes based on shared association of terms and groups those genes into functionally related groups with a novel fuzzy clustering algorithm. As with other tools, options are available for power users and defaults set for quick analyses.
Gene Functional Classification Result
Help and Tool Manual Current Gene List: demolist2 Current Background: Homo sapiens 372 DAVID IDs ■ Options Classification Stringency | Medium ◇
This tool can efficiently convert gene/protein identifiers from one identifier type to another at the gene level. The tool can automatically suggest possible identifier types for ambiguous gene/protein identifiers and converted identifiers can be downloaded or submitted back to DAVID as a gene list or background population set.
Gene Accession Conversion Tool
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Additional Help
. DAVID Documentation Nature Protocols Paper DAVID Forum Contact the DAVID Team