DAVID Bioinformatics 6.7
The Database for Annotation, Visualization and Integrated Discovery
DAVID Bioinformatics Resources 6.7
National Institute of Allergy and Infectious Diseases (NIAID), NIH
acknowledgement
ACKNOWLEDGEMENT

Contributors  to DAVID Development
  • The DAVID bioinformatic team (LIB/CSP at SAIC-Frederick, Inc.) played  primary roles in designing, integrating, deploying and maintaining DAVID and EASE application.
  • Thanks to Mr. Bill Wilton (CSP at SAIC-Frederick, Inc.), Mr. Dmitriy Kholodenko (NIAID, NIH), and Mr. Mike Tartakovsky (NIAID, NIH) for various IT supports.
  • Thanks to Mr. David Bryant (ABCC at SAIC-Frederick, Inc.) for hosting current DAVID web server.
  • Thanks to Mr. David Liu (ABCC at SAIC-Frederick, Inc.) for hosting Oracle database.
  • Thanks to Dr. Jack R. Collins (ABCC at SAIC-Frederick, Inc.) for genome-wide Kappa calculation.
  • Thanks to Dr. Jason Guo and Dr. Stephan Bour (BSSP/OTIS/NIAID) for DAVID knowledge database QC.
  • Thanks to Dr. W. Gregory Alvord (C&SS at SAIC-Frederick, Inc) for various statistical consultation.
  • Thanks to Ms. Jillian Deshazer and Mr. Galen Mayfield  (C&SS at SAIC-Frederick, Inc.) for DAVID logo, graphic & interface works.
  • Thanks to Ms. Jennifer Brown and Ms. Kathy Green (Scientific Publication, Graphics and Media group at SAIC-Frederick, Inc.) for the design of the DAVID logo and general web site design suggestions.

Contributions of Public Data Resources to DAVID Knowledge Base Construction
  • Primary Data Sources: Used for DAVID gene clustering

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NCBI Entrez Gene:  http://www.ncbi.nlm.nih.gov/Entrez/

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UniProt and UniRef100: http://www.pir.uniprot.org/
Swiss-Prot entries are copyrighted. They are produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on their use by non-profit institutions as long as their content is in no way modified and this statement is not removed. Usage by and for commercial entities requires a license agreement (See http://www.isb-sib.ch/announce/ or send an email to license@isb-sib.ch)

-
PIR NREF and iProClass: http://pir.georgetown.edu/

  • Secondary Sources of Annotation: Used to map additional annotation to DAVID Genes


Affymetrix Probeset Mapping
- NetAffx: http://www.netaffx.com/
- TIGR: http://www.tigr.org/tdb/



Ontologies
- Data extract from Entrez Gene, PIR iProClass, UniProt  and GOA records.
- Panther Ontolgoy:  http://www.pantherdb.org/
- Additional information regarding Gene Ontology can be found at http://www.geneontology.org.



Protein Domains
- Data extract from Entrez Gene, PIR iProClass, UniProt and InterPro records.
- Additional information can be found at websites for Pfam, COG/KOG, Blocks, SMARTPDB, ProDom, PROSITE, TIGRFAMs, PRINTS, Panther Family and SCOP.



Pathways:
- KEGG Pathways, KEGG Reaction, KEGG Compound:  http://www.genome.jp/kegg/
- CGAP BioCarta Pathways: http://cgap.nci.nih.gov/Pathways/BioCarta_Pathways  
- Biocarta: http://www.biocarta.com/genes/index.asp
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 - BBID:  http://bbid.grc.nia.nih.gov/ 
 - PID: http://pid.nci.nih.gov/
 - Panther Pathway: http://www.pantherdb.org/
 - REACTOME: http://www.reactome.org/



General Annotation
- Data extract from Entrez Gene, PIR iProClass and/or UniProt.



Functional Categories  
- Data extract from Entrez Gene, PIR iProClass, UniProt and/or COG/KOG. 



Protein Interactions
- HIV Interactions: Entrez Gene and http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
- NCICB caPathway:  http://ncicb.nci.nih.gov
- Bind: http://www.blueprint.org/bind/bind.php
- Mint: http://mint.bio.uniroma2.it/mint/
- HPRD: http://www.hprd.org/
- DIP: http://dip.doe-mbi.ucla.edu
- REACTOME:
http://www.reactome.org/




Literature
- PubMed ID:  Data extract from Entrez Gene, PIR iProClass and/or UniProt.
- GeneRIF: Extracted from Entrez Gene



Disease
- Genetic Association Database:  http://geneticassociationdb.nih.gov/
- OMIM Phenotype:  Entrez Gene and OMIM



Tissue Expression
- GNF Microarray: http://wombat.gnf.org/index.html
- CGAP SAGE: http://cgap.nci.nih.gov/SAGE
- CGAP Tissue EST: http://cgap.nci.nih.gov/Tissues
- NCBI Unigene EST Profile: ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/

 


Other Data Sources
- HomoloGene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene



Funding

This project has been funded with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, under Contract No. NO1-C0-56000.  The contents of this tool does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the United States government.







 Please cite Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 within any publication that makes use of any methods inspired by DAVID.
                          

        

                 
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