Data reporting standards: Making the things we use better

Genome Medicine

Volumn 1, Issue 11, 2009, Pages

  Quackenbush, John ^a  

^a DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DETERMINATION; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION; GENETIC DATABASE; GENOMICS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NOTE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE DATABASE;

EID: 77949887576     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm111     Document Type: Note

References (9)

1. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210.
2. 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, 31:68-71.
3. 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.
4. 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: RESEARCH0046.
5. Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, Jr., White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 2006, 7:489.
6. Landemaine T, Jackson A, Bellahcene A, Rucci N, Sin S, Abad BM, Sierra A, Boudinet A, Guinebretiere JM, Ricevuto E, Nogues C, Briffod M, Bieche I, Cherel P, Garcia T, Castronovo V, Teti A, Lidereau R, Driouch K: A six-gene signature predicting breast cancer lung metastasis. Cancer Res 2008, 68: 6092-6099.
7. Culhane A, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J: GeneSigDB - a curated database of gene expression signatures. Nucl Acids Res 2009, in press.
8. Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, et al.: Prepublication data sharing. Nature 2009, 461:168-170.
9. Schofield PN, Bubela T, Weaver T, Portilla L, Brown SD, Hancock JM, Einhorn D, Tocchini-Valentini G, Hrabe de Angelis M, Rosenthal N: Post-publication sharing of data and tools. Nature 2009, 461:171-173.