A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Rayner, Tim F.; Rocca-Serra, Philippe; Spellman, Paul T.; Causton, Helen C.; Farne, Anna; Holloway, Ele; Irizarry, Rafael A.; Liu, Junmin; Maier, Donald S.; Miller, Michael; Petersen, Kjell; Quackenbush, John; Sherlock, Gavin; Stoeckert, Christian J.; White, Joseph; Whetzel, Patricia L.; Wymore, Farrell; Parkinson, Helen; Sarkans, Ugis; Ball, Catherine A.; Brazma, Alvis

doi:10.1186/1471-2105-7-489

Title: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Journal Article · Mon Nov 06 00:00:00 EST 2006 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-7-489· OSTI ID:1629617

Rayner, Tim F. ^[1]; Rocca-Serra, Philippe ^[1]; Spellman, Paul T. ^[2]; Causton, Helen C. ^[3]; Farne, Anna ^[1]; Holloway, Ele ^[1]; Irizarry, Rafael A. ^[4]; Liu, Junmin ^[5]; Maier, Donald S. ^[6]; Miller, Michael ^[7]; Petersen, Kjell ^[8]; Quackenbush, John ^[9]; Sherlock, Gavin ^[10]; Stoeckert, Christian J. ^[5]; White, Joseph ^[9]; Whetzel, Patricia L. ^[5]; Wymore, Farrell ^[6]; Parkinson, Helen ^[1]; Sarkans, Ugis ^[1]; Ball, Catherine A. ^[6] more »

Wellcome Trust Genome Campus, Hinxton, Cambridge (United Kingdom). European Bioinformatics Inst.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Imperial College, London (United Kingdom). Hammersmith Hospital Campus. MRC Clinical Sciences Centre. Faculty of Medicine
Johns Hopkins Univ., Baltimore, MD (United States). Public Health. Dept. of Biostatistics
Univ. of Pennsylvania, Philadelphia, PA (United States). School of Medicine. Dept. of Genetics. Center for Bioinformatics
Stanford Univ., CA (United States). School of Medicine. Dept. of Biochemistry
Rosetta Inpharmatics, LLC, Seattle, WA (United States). Rosetta Biosoftware
Univ. of Bergen (Norway). Computational Biology Unit. Begen Center for Computational Science
Dana Farber Cancer Institute, Boston, MA (United States)
Stanford Univ., CA (United States). Dept. of Genetics

Background: Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGEML by the MGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support. Results: We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion. Conclusion: MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; NHGRI; NIBIB; European Commission (EC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1629617

Journal Information:: BMC Bioinformatics, Vol. 7, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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