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A comparative account of gene expression resources, feature-validations and application-based categorizations : EST
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
TiGER - Tissue-specific Gene Expression and Regulation
http://bioinfo.wilmer.jhu.edu/tiger
A database for tissue-specific gene expression and regulation. It contains three types of data: tissue-specific gene expression profiles (based on EST data), combinatorial gene regulations, and cis-regulatory module detections. It has gene view, transcription factor view and tissue view. It also provides the preferential expression site for the queried gene.
Liu X, Yu X, Zack DJ, Zhu H, Qian J. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics. 2008 Jun 9;9:271. PubMed PMID: 18541026; PubMed Central PMCID: PMC2438328.
2008
92
GeneCards
http://www.genecards.org
A human gene compendium that provides gene related information such as function, pathways, expression and interactions for all known and predicted human genes.
Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet. 1997 Apr;13(4):163. PubMed PMID: 9097728.
1997
97
Note as per the resource: "The service is provided free to academic non-profit institutions. All other users require a Commercial License from XenneX, Inc. Unauthorized usage of this service is in breach of the terms and conditions of this web site, and may cause the user to incur fees for usage".
UniGene
http://www.ncbi.nlm.nih.gov/unigene
A database that provides gene expression at EST level, for various normal and disease tissues, and developmental stages. The level of expression is indicated by transcripts per million (TPM).
Boguski MS, Schuler GD. ESTablishing a human transcript map. Nat Genet. 1995 Aug;10(4):369-71. PubMed PMID: 7670480.
1995
98
Bgee - a dataBase for Gene Expression Evolution
http://bgee.unil.ch
A database to retrieve and compare gene expression patterns between animal species, currrently covering five, including human and mouse. Bgee maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization) on anatomical and developmental ontologies.
Parmentier G, Bastian FB, Robinson-Rechavi M. Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics. 2010 Jul 15;26(14):1766-71. Epub 2010 Jun 2. PubMed PMID: 20519284; PubMed Central PMCID: PMC2894521.
2010
100
TissueDistributionDBs
http://genome.dkfz-heidelberg.de/menu/tissue_db
A repository of tissue distribution profiles that identifies and ranks genes in the spectrum of tissue specificity, based on Expressed Sequence Tags (ESTs) data. The database provides information on tissue specific genes, housekeeping genes and a small number of tissues that can be said to share the gene at a certain specificity level. The database currently has many model plant and animal species.
Not available
Not available
100
TiProD - Tissue specific Promoter Database
http://tiprod.bioinf.med.uni-goettingen.de
A database that retrieves promoter sequences according to their tissue-specificity or other functional groupings. TiPROD uses the CGAP (Cancer Genome Anatomy Project) data and calculates tissue-specific gene expression for healthy tissues and assigns these tissue specificity to their corresponding regulatory regions based on EPD, DBTSS, and Ensembl annotation. Gene Ontology terms or ID can also be queried, other than UniGene ID.
Chen X, Wu JM, Hornischer K, Kel A, Wingender E. TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D104-7. PubMed PMID: 16381824; PubMed Central PMCID: PMC1347475.
2006
100
 
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