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. 2004 Aug-Oct;5(6-7):471–479. doi: 10.1002/cfg.427

Navigating Public Microarray Databases

Christopher J Penkett 1,✉, Jürg Bähler 1
PMCID: PMC2447434  PMID: 18629145

Abstract

With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources.

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Selected References

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  1. Aach J., Rindone W., Church G. M. Systematic management and analysis of yeast gene expression data. Genome Res. 2000 Apr;10(4):431–445. doi: 10.1101/gr.10.4.431. [DOI] [PubMed] [Google Scholar]
  2. Anderle Pascale, Duval Manuel, Draghici Sorin, Kuklin Alexander, Littlejohn Timothy G., Medrano Juan F., Vilanova David, Roberts Matthew Alan. Gene expression databases and data mining. Biotechniques. 2003 Mar;Suppl:36–44. [PubMed] [Google Scholar]
  3. Bahl Amit, Brunk Brian, Crabtree Jonathan, Fraunholz Martin J., Gajria Bindu, Grant Gregory R., Ginsburg Hagai, Gupta Dinesh, Kissinger Jessica C., Labo Philip. PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 2003 Jan 1;31(1):212–215. doi: 10.1093/nar/gkg081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Ball C. A., Jin H., Sherlock G., Weng S., Matese J. C., Andrada R., Binkley G., Dolinski K., Dwight S. S., Harris M. A. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80–81. doi: 10.1093/nar/29.1.80. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Ball Catherine A., Brazma Alvis, Causton Helen, Chervitz Steve, Edgar Ron, Hingamp Pascal, Matese John C., Parkinson Helen, Quackenbush John, Ringwald Martin. Submission of microarray data to public repositories. PLoS Biol. 2004 Aug 31;2(9):E317–E317. doi: 10.1371/journal.pbio.0020317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ball Catherine A., Sherlock Gavin, Brazma Alvis. Funding high-throughput data sharing. Nat Biotechnol. 2004 Sep;22(9):1179–1183. doi: 10.1038/nbt0904-1179. [DOI] [PubMed] [Google Scholar]
  7. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C. A., Causton H. C. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec;29(4):365–371. doi: 10.1038/ng1201-365. [DOI] [PubMed] [Google Scholar]
  8. Brazma A., Robinson A., Cameron G., Ashburner M. One-stop shop for microarray data. Nature. 2000 Feb 17;403(6771):699–700. doi: 10.1038/35001676. [DOI] [PubMed] [Google Scholar]
  9. Brazma Alvis, Parkinson Helen, Sarkans Ugis, Shojatalab Mohammadreza, Vilo Jaak, Abeygunawardena Niran, Holloway Ele, Kapushesky Misha, Kemmeren Patrick, Lara Gonzalo Garcia. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003 Jan 1;31(1):68–71. doi: 10.1093/nar/gkg091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Chalifa-Caspi Vered, Shmueli Orit, Benjamin-Rodrig Hila, Rosen Naomi, Shmoish Michael, Yanai Itai, Ophir Ron, Kats Pavel, Safran Marilyn, Lancet Doron. GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia. Brief Bioinform. 2003 Dec;4(4):349–360. doi: 10.1093/bib/4.4.349. [DOI] [PubMed] [Google Scholar]
  11. Chen Josephine, Zhao Po, Massaro Donald, Clerch Linda B., Almon Richard R., DuBois Debra C., Jusko William J., Hoffman Eric P. The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D578–D581. doi: 10.1093/nar/gkh003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cheung Kei-Hoi, White Kevin, Hager Janet, Gerstein Mark, Reinke Valerie, Nelson Kenneth, Masiar Peter, Srivastava Ranjana, Li Yuli, Li Ju. YMD: a microarray database for large-scale gene expression analysis. Proc AMIA Symp. 2002:140–144. [PMC free article] [PubMed] [Google Scholar]
  13. Craigon David J., James Nick, Okyere John, Higgins Janet, Jotham Joan, May Sean. NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D575–D577. doi: 10.1093/nar/gkh133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dudoit Sandrine, Gentleman Robert C., Quackenbush John. Open source software for the analysis of microarray data. Biotechniques. 2003 Mar;Suppl:45–51. [PubMed] [Google Scholar]
  15. Edgar Ron, Domrachev Michael, Lash Alex E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002 Jan 1;30(1):207–210. doi: 10.1093/nar/30.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gardiner-Garden M., Littlejohn T. G. A comparison of microarray databases. Brief Bioinform. 2001 May;2(2):143–158. doi: 10.1093/bib/2.2.143. [DOI] [PubMed] [Google Scholar]
  17. Gollub Jeremy, Ball Catherine A., Binkley Gail, Demeter Janos, Finkelstein David B., Hebert Joan M., Hernandez-Boussard Tina, Jin Heng, Kaloper Miroslava, Matese John C. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 2003 Jan 1;31(1):94–96. doi: 10.1093/nar/gkg078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Grimmond Sean M., Miranda Kevin C., Yuan Zheng, Davis Melissa J., Hume David A., Yagi Ken, Tominaga Naoko, Bono Hidemasa, Hayashizaki Yoshihide, Okazaki Yasushi. The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Genome Res. 2003 Jun;13(6B):1350–1359. doi: 10.1101/gr.983703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Harrison Rhonda, DeLisi Charles. Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. Bioinformatics. 2002 Oct;18(10):1289–1296. doi: 10.1093/bioinformatics/18.10.1289. [DOI] [PubMed] [Google Scholar]
  20. Haverty Peter M., Weng Zhiping, Best Nathan L., Auerbach Kenneth R., Hsiao Li-Li, Jensen Roderick V., Gullans Steven R. HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Res. 2002 Jan 1;30(1):214–217. doi: 10.1093/nar/30.1.214. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hertz-Fowler Christiane, Peacock Chris S., Wood Valerie, Aslett Martin, Kerhornou Arnaud, Mooney Paul, Tivey Adrian, Berriman Matthew, Hall Neil, Rutherford Kim. GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D339–D343. doi: 10.1093/nar/gkh007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ikeo Kazuho, Ishi-i Jun, Tamura Takurou, Gojobori Takashi, Tateno Yoshio. CIBEX: center for information biology gene expression database. C R Biol. 2003 Oct-Nov;326(10-11):1079–1082. doi: 10.1016/j.crvi.2003.09.034. [DOI] [PubMed] [Google Scholar]
  23. Kaestner Klaus H., Lee Catherine S., Scearce L. Marie, Brestelli John E., Arsenlis Athanasios, Le Phillip Phuc, Lantz Kristen A., Crabtree Jonathan, Pizarro Angel, Mazzarelli Joan. Transcriptional program of the endocrine pancreas in mice and humans. Diabetes. 2003 Jul;52(7):1604–1610. doi: 10.2337/diabetes.52.7.1604. [DOI] [PubMed] [Google Scholar]
  24. Lelandais Gaëlle, Le Crom Stéphane, Devaux Frédéric, Vialette Stéphane, Church George M., Jacq Claude, Marc Philippe. yMGV: a cross-species expression data mining tool. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D323–D325. doi: 10.1093/nar/gkh135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mantripragada Kiran K., Buckley Patrick G., Diaz de Ståhl Teresita, Dumanski Jan P. Genomic microarrays in the spotlight. Trends Genet. 2004 Feb;20(2):87–94. doi: 10.1016/j.tig.2003.12.008. [DOI] [PubMed] [Google Scholar]
  26. Moreau Yves, Aerts Stein, De Moor Bart, De Strooper Bart, Dabrowski Michal. Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet. 2003 Oct;19(10):570–577. doi: 10.1016/j.tig.2003.08.006. [DOI] [PubMed] [Google Scholar]
  27. Pollack Jonathan R., Iyer Vishwanath R. Characterizing the physical genome. Nat Genet. 2002 Dec;32 (Suppl):515–521. doi: 10.1038/ng1035. [DOI] [PubMed] [Google Scholar]
  28. Praz Viviane, Jagannathan Vidhya, Bucher Philipp. CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D542–D547. doi: 10.1093/nar/gkh107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rocca-Serra Philippe, Brazma Alvis, Parkinson Helen, Sarkans Ugis, Shojatalab Mohammadreza, Contrino Sergio, Vilo Jaak, Abeygunawardena Niran, Mukherjee Gaurab, Holloway Ele. ArrayExpress: a public database of gene expression data at EBI. C R Biol. 2003 Oct-Nov;326(10-11):1075–1078. doi: 10.1016/j.crvi.2003.09.026. [DOI] [PubMed] [Google Scholar]
  30. Saeed A. I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374–378. doi: 10.2144/03342mt01. [DOI] [PubMed] [Google Scholar]
  31. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  32. Schulze A., Downward J. Navigating gene expression using microarrays--a technology review. Nat Cell Biol. 2001 Aug;3(8):E190–E195. doi: 10.1038/35087138. [DOI] [PubMed] [Google Scholar]
  33. Searls D. B. Bioinformatics tools for whole genomes. Annu Rev Genomics Hum Genet. 2000;1:251–279. doi: 10.1146/annurev.genom.1.1.251. [DOI] [PubMed] [Google Scholar]
  34. Spellman P. T. The future of publishing microarray data. Brief Bioinform. 2001 Dec;2(4):316–318. doi: 10.1093/bib/2.4.316. [DOI] [PubMed] [Google Scholar]
  35. Stoeckert C., Pizarro A., Manduchi E., Gibson M., Brunk B., Crabtree J., Schug J., Shen-Orr S., Overton G. C. A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics. 2001 Apr;17(4):300–308. doi: 10.1093/bioinformatics/17.4.300. [DOI] [PubMed] [Google Scholar]
  36. Stoeckert Christian J., Jr, Causton Helen C., Ball Catherine A. Microarray databases: standards and ontologies. Nat Genet. 2002 Dec;32 (Suppl):469–473. doi: 10.1038/ng1028. [DOI] [PubMed] [Google Scholar]
  37. Su Andrew I., Cooke Michael P., Ching Keith A., Hakak Yaron, Walker John R., Wiltshire Tim, Orth Anthony P., Vega Raquel G., Sapinoso Lisa M., Moqrich Aziz. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002 Mar 19;99(7):4465–4470. doi: 10.1073/pnas.012025199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Su Andrew I., Wiltshire Tim, Batalov Serge, Lapp Hilmar, Ching Keith A., Block David, Zhang Jie, Soden Richard, Hayakawa Mimi, Kreiman Gabriel. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 9;101(16):6062–6067. doi: 10.1073/pnas.0400782101. [DOI] [PMC free article] [PubMed] [Google Scholar]

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