Related Experiment Video
Updated: Jul 10, 2026
07:35
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
Published on: October 11, 2018
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate
Brad T Sherman1, Da Wei Huang, Qina Tan
1Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA. bsherman@mail.nih.gov
BMC Bioinformatics
|November 6, 2007
Summary
The DAVID Knowledgebase centralizes gene annotation data from multiple sources, simplifying high-throughput functional analysis for researchers. This integrated resource enhances biological information accessibility and gene analysis efficiency.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Biological knowledge is fragmented across numerous redundant annotation databases.
- Integrating comprehensive gene annotation information is challenging for large gene lists.
- A centralized, ready-to-use gene annotation knowledgebase is needed for high-throughput analysis.
Purpose of the Study:
- To develop a centralized knowledgebase for gene annotation.
- To facilitate high-throughput gene functional analysis.
- To improve accessibility and integration of diverse biological data.
Main Methods:
- The DAVID Knowledgebase uses the DAVID Gene Concept to cluster gene/protein identifiers.
- Agglomerates identifiers from public genomic resources, enhancing cross-referencing (e.g., NCBI, UniProt).
- Integrates over 40 functional annotation sources into centralized DAVID gene clusters.
Main Results:
- The DAVID Knowledgebase provides centralized access to heterogeneous annotation data.
- Enriches biological information for individual genes.
- Freely downloadable, pair-wise text files and a web interface for querying annotations.
Conclusions:
- The DAVID Knowledgebase facilitates high-throughput gene functional analysis.
- Offers quick access to diverse annotation data in one location.
- Enhances biological information and supports efficient gene list analysis.
Related Concept Videos
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...