acknowledgement
ACKNOWLEDGEMENT
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| 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.
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| 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)
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-
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PIR NREF and iProClass: http://pir.georgetown.edu/
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- Secondary Sources of Annotation: Used to map additional
annotation to DAVID Genes
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Affymetrix
Probeset Mapping
- NetAffx: http://www.netaffx.com/
- TIGR: http://www.tigr.org/tdb/
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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.
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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, SMART,
PDB, ProDom, PROSITE, TIGRFAMs,
PRINTS, Panther Family and SCOP.
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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
The BioCarta Site, including all of its
contents, such as text, images, and the HTML used to generate the
pages, ("Materials"), are protected by patent, trademark and/or
copyright under United States and/or foreign laws. Except as otherwise
provided herein, you may not use, download, upload, copy, print,
display, perform, reproduce, publish, license, post, transmit, or
distribute any Materials from this Site in whole or in part, for any
commercial purpose without the specific permission of BioCarta, Inc.
You may use, download, upload, copy, print, display, perform,
reproduce, publish, license, post, transmit, or distribute any
Materials from this Site in whole or in part, for a public,
noncommercial purpose with the specific permission of BioCarta, Inc.
and/or acknowledgement of BioCarta and citation of the pathway number.
BioCarta claims no ownership rights in the content placed on the Site
by you or other registered users. We grant you a personal,
non-exclusive, non-transferable license to access our web site and the
information contained here. Our site may contain software tools or
databases that allow you to search and retrieve information. You may
not sell, rent, lease, lend, transfer, any services provided on this
site and you may not assign or sublicense this license.
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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/
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General Annotation
- Data extract from Entrez Gene, PIR
iProClass and/or UniProt.
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Functional Categories
- Data extract from Entrez
Gene, PIR
iProClass, UniProt
and/or COG/KOG.
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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/
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Literature
- PubMed ID: Data
extract from Entrez Gene,
PIR
iProClass and/or UniProt.
- GeneRIF: Extracted
from Entrez Gene
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Disease
- Genetic
Association
Database: http://geneticassociationdb.nih.gov/
- OMIM Phenotype: Entrez Gene
and OMIM
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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/
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Other Data Sources
- HomoloGene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
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Funding
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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. |
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