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A comparative account of gene expression resources, feature-validations and application-based categorizations : Plant
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
GEO - Gene Expression Omnibus
http://www.ncbi.nlm.nih.gov/geo
A public genomics data repository that supports MIAME-compliant data submissions. Sequence- and array-based data are accepted. It archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput data. It provides various web-interfaces and applications to query and download the data in GEO.
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002 Jan 1;30 (1):207-10. PubMed PMID: 11752295; PubMed Central PMCID: PMC99122.
2002
1
UniProtKB/Swiss-Prot
http://www.uniprot.org/uniprot
A universal catalog of protein information on function, sequence, expression, and many others. It has two sections: "UniProtKB/Swiss-Prot" containing manually-annotated records and "UniProtKB/TrEMBL" with computationally analyzed records awaiting manual annotation.
Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 1996 Jan 1;24(1):21-5. PubMed PMID: 8594581; PubMed Central PMCID: PMC145613.
1996
96
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
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
COXPRESdb
http://coxpresdb.hgc.jp
A database for co-expressed genes and networks in various species. Four types of co-expression networks can be generated: (i) highly co-expressed genes for every gene, (ii) genes with the same Gene Ontology annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. It also provides a view to compare the co-expression patterns across species to estimate the conservation between the two species. It helps in making gene lists for a particular biological function, and functional estimation of a gene. Currently it covers seven model animals and one plant model.
Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K. COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res. 2008 Jan;36(Database issue):D77-82. Epub 2007 Oct 11. PubMed PMID: 17932064; PubMed Central PMCID: PMC2238883.
2007
100
ArrayExpress
http://www.ebi.ac.uk/arrayexpress
A database of functional genomics experiments with MIAME and MINSEQE standards. The data can be queried and downloaded. Gene Expression Atlas contains a subset of curated and re-annotated archive data, which can be queried for individual gene expression under different biological conditions across experiments.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003 Jan 1;31(1):68-71. PubMed PMID: 12519949; PubMed Central PMCID: PMC165538.
2003
100
SMD - Stanford Microarray Database
http://smd.stanford.edu
A database that stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data.
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Res. 2001 Jan 1;29(1):152-5. PubMed PMID: 11125075; PubMed Central PMCID: PMC29818.
2001
100
Note as per the resource: "Access to non-public data is limited to registered Stanford researchers and their collaborators".
CIBEX
http://cibex.nig.ac.jp
A public repository for a wide range of gene expression high-throughput experimental data, including microarray-based experiments, SAGE, and mass spectrometry proteomic data. It is aimed at storing MIAME-compliant microarray data.
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. CIBEX: center for information biology gene expression database. C R Biol. 2003 Oct-Nov;326(10-11):1079-82. PubMed PMID: 14744116.
2003
100
 
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