Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract The Database for Annotation, Visualization and Integrated Discovery (DAVID) 2008 is the sixth version of the original web- accessible software.

DAVID provides a comprehensive set of 'Functional Annotation Tools' for investigators to understand biological meaning behind a large list of genes.

For any given gene list, DAVID tools are able to:

1) Identify enriched biological themes, particularly Gene Ontology (GO) terms;

2) Discover enriched functional-related gene groups;

3) Cluster redundant annotation terms;

4) Visualize genes on BioCarta & KEGG pathway maps;

5) Display related many-genes-to-many-terms on a 2-D view;

6) Search for other functionally related genes Not in the list;

7) List interacting proteins;

8) Explore gene names in batch;

9) Link gene-disease associations;

10) Highlight protein functional domains and motifs;

11) Redirect to related literature; and

12) Convert gene identifiers from one type to another.

Functional Annotation Tools -- Key Concepts/Features:

The DAVID Gene Concept - DAVID 2.0 is designed around the "DAVID Gene Concept", a graph theory evidence-based method to agglomerate species-specific gene/protein identifiers from a variety of public genomic resources including NCBI, PIR (Protein Information Resource) and Uniprot/SwissProt.

The DAVID Gene Concept method groups tens of million of identifiers from over 65,000 species into 1.5 million unique protein/gene records.

Term/Gene Co-Occurrence Probability - Ranking functional categories based on co-occurrence with sets of genes in a gene list can rapidly aid in unraveling new biological processes associated with cellular functions and pathways.

DAVID 2.0 allows investigators to sort gene categories from dozens of annotation systems.

Sorting can be based on either the number of genes within each category or by the EASE-score (EASE-score - is an alternative name of Fisher Exact Statistics in the DAVID system, referring to a one-tail Fisher Exact Probability Value used for gene-enrichment analysis).

Gene Similarity Search - Any given gene is associated with a set of annotation terms. If the genes share a similar set of those terms, they are most likely involved in similar biological mechanisms.

The algorithm tries to group those related genes based on the agreement of sharing similar annotation terms by Kappa statistics.

Term Similarity Search - Typically, a biological process/term is a cooperation of a set of genes. If two or more 'biological processes' are done by a similar set of genes, the processes might be related in the biological network somehow.

This search function is used to identify the related biological processes/terms by quantitatively measuring the degree of the agreement of how terms share the similar participating genes.

DAVID Annotation Categories -- DAVID 2.0 contains over 40 annotation categories, including GO terms, protein-protein interactions, protein functional domains, disease associations, bio-pathways, sequence general features, homologies, gene functional summaries, gene tissue expressions, literatures, etc.

DAVID Functional Annotation Clustering -- This function uses a novel algorithm to measure relationships among the annotation terms based on the degrees of their co-association genes to group the similar, redundant, and heterogeneous annotation contents from the same or different resources into annotation groups.

This reduces the burden of associating similar redundant terms and makes the biological interpretation more focused in a group level.

DAVID Pathway Viewer -- Using well-known KEGG and BioCarta pathways, the DAVID Pathway Viewer, can display genes from a user’s list on pathway maps to facilitate biological interpretation in a network context.

Gene Functional Classification -- Grouping genes based on functional similarity can systematically enhance biological interpretation of large lists of genes derived from high throughput studies.

The Functional Classification Tool (FCT) generates a gene-to-gene similarity matrix based shared functional annotation using over 75,000 terms from 14 functional annotation sources.

The manufacturer’s novel clustering algorithms can classify highly related genes into functionally related groups.

Tools are also provided to further explore each functional gene cluster including the listing of the “consensus terms” shared by the genes in the cluster, display of enriched terms, and 'heat map visualization' of gene-to-term relationships.

A global view of cluster-to-cluster relationships is provided using 'fuzzy heat map’ visualization. Summary information provided by the FCT is extensively linked to DAVID Functional Annotation Tools and to external databases allowing further detailed exploration of gene and term information.

The FCT provides a rapid means to organize large lists of genes into functionally related groups to help unravel the biological content captured by high throughput technologies.

DAVID Gene Accession Conversion Tool -- This tool was built based on the 'DAVID Gene Concept' (see above). With this comprehensive accession mapping system, any given gene accession can be quickly mapped to another based on the user's choice.

The tool also automatically suggests possible choices for the ambiguous gene accessions in the list.

Gene Name Batch Viewer --

1) Lets you quickly translate given gene IDs to corresponding gene names in a batch way;

2) Provides links for each gene to the DAVID Gene Report for in-depth information; and

3) Allows you to search functionally related genes within the user's input gene list or genome.

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