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Created on: 07-Jun-2011   Last updated on: 14-Dec-2011  |  How to cite this?
Total resources - 16
A compilation of Gene ID conversion resources
Judith Mary. H., S. Seetha Lakshmi and R. Shobana (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
NetAffx™
http://www.affymetrix.com/analysis/index.affx
Registration is required. It has batch and net affx query, provides detailed description of individual probeset and allows user to group probsets according to annotation type. Covers 10 species and has 17 possible conversions.
Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 2003 Jan 1;31(1):82-6. PubMed PMID: 12519953; PubMed Central PMCID: PMC165568.
2003
30
g:Profiler
http://biit.cs.ut.ee/gprofiler/gconvert.cgi
Input can be a mix of different ID types. User has to choose only the desired output. It covers 31 species and has 14 possible conversions.
Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200. Epub 2007 May 3.PubMed PMID: 17478515;
2007
39
Babelomics ID-Converter
http://babelomics3.bioinfo.cipf.es/
GeneID alone as input ID type. Covers 11 species and 36 output ID types are available.
Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W210-3. Epub 2010 May 16. PubMed PMID: 20478823
2010
63
SOURCE
http://smd.stanford.edu/cgi-bin/source/sourceSearch
Provides either the clone or gene report. Links to UCSC Genome Browser from human gene reports are available. It covers 3 species and has 2 possible conversions.
Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 2003 Jan 1;31(1):219-23. PubMed PMID: 12519986;
2003
65
PICR - Protein Identifier Cross-Referencing Service
http://www.ebi.ac.uk/Tools/picr/
Covers 58 species. Input can be either an accession number or a sequence. It has 24 possible conversions.
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H. BMC Bioinformatics. 2007 Oct 18;8:401. PMID: 17945017
2007
66
DAVID Gene ID Conversion Tool
http://david.abcc.ncifcrf.gov/conversion.jsp
User can upload more than one file of different ID types. A specific format is not available and it has 32 possible conversion.
DAVID gene ID conversion tool. Huang da W, Sherman BT, Stephens R, Baseler MW, Lane HC, Lempicki RA. Bioinformation. 2008 Jul 30;2(10):428-30. PubMed PMID: 18841237
2008
71
ONTO-TRANSLATE™
http://vortex.cs.wayne.edu/ontoexpress/
Requires registration and runs on a Java plugin. It covers 59 species and has 27 possible conversions.
Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res. 2003 Jul 1;31(13):3775-81. PubMed PMID:12824416
2003
81
Clone/Gene ID Converter
http://idconverter.bioinfo.cnio.es/
Gene ontology, pathway and literature references are available. Provides chromosome location for human. Covers 3 species and has 25 possible conversions.
Imanishi T, Nakaoka H. Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W17-22. Epub 2009 May 19. PubMed PMID:19454601;
2009
89
CRONOS
http://mips.helmholtz-muenchen.de/genre/proj/cronos/batch.html
Provides batch or single input query. It covers 6 species and has 20 possible conversions.
CRONOS the cross-reference navigation server.Waegele B, Dunger-Kaltenbach I, Fobo G, Montrone C, Mewes HW, Ruepp A. BioInformatics. 2009 Jan 1;25(1):141-3. Epub 2008 Nov 13. PubMed PMID: 19010804
2009
92
MatchMiner
http://discover.nci.nih.gov/matchminer/MatchMinerLookup.jsp
It combines two separate lists of either the same or different types of identifiers into one list that details all one-to-one, one-to-many, and many-to-many relationships between corresponding gene identifiers in the two lists. Covers 2 species and has 22 possible conversions.
Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN. MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol. 2003;4(4):R27. Epub 2003 Mar 25. PubMed PMID: 12702208;
2003
93
Synergizer
http://llama.mshri.on.ca/synergizer/translate/
It is a repository of gene and protein identifier synonym relationships. The number of species covered changes based on the 'authority' used and accordingly the number of input and output format also change.
The Synergizer service for translating gene, protein and other biological identifiers. Bioinformatics. 2008 Oct 1;24(19):2272-3. Epub 2008 Aug 12. PubMed PMID: 18697767
2008
93
MADGene
http://cardioserve.nantes.inserm.fr/mad/madgene/
It is formed by parsing Hugo, Unigene, EntrezGene, Homologene, Ensembl, UniProt and GEO repository. Covers 17 species, contains a feature of inter-species conversion and has 13 possible conversions.
Baron D, Bihouée A, Teusan R, Dubois E, Savagner F, Steenman M, Houlgatte R,Ramstein G. MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets. Bioinformatics. 2011 Mar1;27(5):725-6. Epub 2011 Jan 6. PubMed PMID: 21216776;
2011
95
ID Converter System
http://biodb.jp/#ids
Covers 2 species viz., human and mouse. Around 24 output ID types are available.
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Imanishi T, Nakaoka H. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W17-22. Epub 2009 May 19 PMID: 19454601.
2009
97
GeneALAcart™
http://www.genecards.org/cgi-bin/BatchQueries/Batch.pl
Registration is required. Only 100 genes can be retrieved each day for the beta version. License is provided by Xennex Sales for the commercial usage. Orthologs, paralogs, drug bank, pathway, chromosome location is also available. Covers 53 possible conversions only from human.
Chalifa-Caspi V, Shmueli O, Benjamin-Rodrig H, Rosen N, Shmoish M, Yanai I,Ophir R, Kats P, Safran M, Lancet D. GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia. Brief Bioinform. 2003 Dec;4(4):349-60. PubMed PMID: 14725348
2003
98
ReMOAT
http://remoat.sysbiol.cam.ac.uk/search.php
Link to WikiGenes and iHop is available. It maps Illumina, Ensembl and Entrez gene IDs into other ID formats and covers human species (human, mouse, and rat for Illumina alone).
Not available
Not available
99
DRAGON
Registration is required. It has batch and net affx query, provides detailed description of individual probeset and allows user to group probsets according to the annotation type. Covers 1 species and has 15 possible conversions.
Bouton CM, Pevsner J. DRAGON and DRAGON view: information annotation and visualization tools for large-scale expression data. Curr Protoc Bioinformatics. 2003 Aug;Chapter 7:Unit 7.4. PubMed PMID: 18428707.
2003
100
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