LY incorporated protein structure manipulative tools for the database.
The functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID, david.abcc.ncifcrf.gov) was used to search for clusters of biological processes of the GO database within two sets of differentially expressed genes, namely HCID vs. HCIS and CXID vs. CXIS (http://david.abcc.ncifcrf.gov) [34], [35].
The gene ontology (GO) cluster analysis of all mutated genes was done using the Functional Annotation Tool of the Database for Annotation, Visualization and Integrated Discovery (DAVID) [59].
The functional analysis and clustering tool from the Database for Annotation, Visualisation, and Integrated Discovery (DAVID bioinformatics resources 6.7) was used [ 27].
The functional annotation tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID) bioinformatics resource [ 73] (http://david.abcc.ncifcrf.gov/) was used to analyse target genes of interest, whether predicted and/or identified from differential gene expression analysis, and used to identify significantly enriched KEGG pathways against a homo sapiens background.
The ribosomal DNA (rDNA) database is composed of a MySQL database and a web-based tool for querying the database.
We used the functional gene annotation tools from the Database for Annotation, Visualization and Integrated Discovery (DAVID) [ 36] to test for both enriched biochemical pathways and subcellular compartmentalization.
A series of further workshops culminated in June 1999 with the establishment of a scientific steering committee of prominent marine scientists that met in Paris in 2000 and enumerated the specific goals of the census: (1) centralize existing knowledge in an Internet database, (2) create analytical tools for querying the database, and (3) determine how to implement new technology in field studies.
Interestingly, in a recent article, Jefferson et al. [ 15] describe tools for the CAMBIA database that begin to address this very issue.
For the gene list in DEPs and DEGs, a functional annotation tool called the Database for Annotation, Visualization and Integrated Discovery (DAVID) [ 24] was applied to find functionally enriched terms.
