Acharya et al. BMC Genomics 2010, 11:467 http://www.biomedcentral.com/1471-2164/11/467 work, solved difficult cases of biocuration, identified the database components and designed broad structure, coordinated the events, supervised the progress of the work of the entire team and wrote the manuscript. DSC created the database and the associated software, and interfaced with biocurators. HS and VM also contributed towards database creation. NC performed biocuration, contributed significantly in training members and coordinating biocuration and data-validation efforts, and also contributed to the design of the database and its validation. SKS, DH, AB, SD, PB and LR contributed to biocuration, data collection and cross- validations. SKS, DH, AB and SD also contributed to manuscript writing. All authors read and approved the final manuscript. Received: 3 March 2010 Accepted: 11 August 2010 Published: 11 August 2010 References 1. Boguski MS, Schuler GD: ESTablishing a human transcript map. Nat Genet 1995, 10:369-371. 2. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB: Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 2002, 99:4465-4470. 3. Lee TL, Cheung HH, Claus J, Sastry C, Singh S, Vu L, Rennert O, Chan WY: GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development. Nucleic Acids Res 2009, 37:D891-D897. 4. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A: Human Protein Reference Database–2009 update. Nucleic Acids Res 2009, 37:D767-D772. 5. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martínez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple- laboratory comparison of microarray platforms. Nat Methods 2005, 2:345-350. 6. Shi L, Tong W, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Guo L, Su Z, Han T, Fuscoe JC, Xu ZA, Patterson TA, Hong H, Xie Q, Perkins RG, Chen JJ, Casciano DA: Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 2005, 6(Suppl 2):S12. 7. Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G 3rd, McCaffrey TA: Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007, 401:12-18. 8. Wilkes T, Laux H, Foy CA: Microarray data quality - review of current developments. OMICS 2007, 11:1-13. 9. Wilder SP, Kaisaki PJ, Argoud K, Salhan A, Ragoussis J, Bihoreau MT, Gauguier D: Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes. BMC Genomics 2009, 10:63. 10. Larsson O, Sandberg R: Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol 2006, 24:1322-1323. 11. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM: ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 2004, 6:1-6. 12. Petrusz P, Jeyaraj DA, Grossman G: Microarray analysis of androgen- regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model. Reprod Biol Endocrinol 2005, 3:70. 13. Sadate-Ngatchou PI, Pouchnik DJ, Griswold MD: Follicle-stimulating hormone induced changes in gene expression of murine testis. Mol Endocrinol 2004, 18:2805-2816. 14. Almstrup K, Hoei-Hansen CE, Nielsen JE, Wirkner U, Ansorge W, Skakkebaek NE, Rajpert-De Meyts E, Leffers H: Genome-wide gene expression profiling of testicular carcinoma in situ progression into overt tumours. Br J Cancer 2005, 92:1934-1941. Page 9 of 10 15. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R: NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, 37:D885-D890. 16. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A: ArrayExpress update– from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009, 37:D868-D872. 17. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA: The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007, 35:D766-D770. 18. Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y: CIBEX: center for information biology gene expression database. C R Biol 2003, 326:1079-1082. 19. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-370. 20. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K: DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res 2008, 36: D97-D101. 21. Lopez F, Textoris J, Bergon A, Didier G, Remy E, Granjeaud S, Imbert J, Nguyen C, Puthier D: TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS One 2008, 3:e4001. 22. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P: Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 2008, 2008:420747. 23. 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, 36:D77-D82. 24. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29:365-371. 25. Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A: Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 2002, 3:0046.1-0046.9. 26. Yauk CL, Berndt ML: Review of the literature examining the correlation among DNA microarray technologies. Environ Mol Mutagen 2007, 48:380-394. 27. Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V: Repeatability of published microarray gene expression analyses. Nat Genet 2009, 41:149-155. 28. Wren JD: A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics 2009, 25:1694-1701. 29. Ramasamy A, Mondry A, Holmes CC, Altman DG: Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008, 5:e184. 30. Smith DD, Saetrom P, Snøve O Jr, Lundberg C, Rivas GE, Glackin C, Larson GP: Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation. BMC Bioinformatics 2008, 9:63. 31. Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LD, Goel R, Mathivanan S, Marimuthu A, Kashyap M, Vizza RF, Mayer RJ, Decaprio JA,