SBEAMS-Microarray: Database software supporting genomic expression analyses for systems biology

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Marzolf, Bruz ^a   Deutsch, Eric W ^a   Moss, Patrick ^a   Campbell, David ^a   Johnson, Michael H ^a   Galitski, Timothy ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INFORMATION; EXPERIMENT ANALYSIS; GENOMIC EXPRESSION; INTERACTING MOLECULES; MODELING SOFTWARES; NETWORK BASED SYSTEMS; NETWORK INTEGRATION; OPEN SOURCE SYSTEM;

BIOLOGY; DATA INTEGRATION; DIGITAL STORAGE; GENES; INTEGRATION;

INFORMATION MANAGEMENT;

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; COMPUTER INTERFACE; COMPUTER NETWORK; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETIC DATABASE; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; INFORMATION STORAGE; INTERNET; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; SYSTEMS BIOLOGY; CHROMOSOME MAP; DNA MICROARRAY; INFORMATION RETRIEVAL; PROCEDURES; PROTEIN DATABASE;

CHROMOSOME MAPPING; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; SYSTEMS BIOLOGY; USER-COMPUTER INTERFACE;

EID: 33746704351     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-286     Document Type: Article

References (31)

1. Galitski T: Molecular networks in model systems. Annu Rev Genomics Hum Genet 2004, 5:177-187.
2. Ideker T, Galitski T, Hood L: A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2001, 2:343-372.
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(4):365-371.
4. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504.
5. Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C: BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol 2002, 3(8):SOFTWARE0003.
6. Killion PJ, Sherlock G, Iyer VR: The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics 2003, 4:32.
7. Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z: MARS: microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005, 6(1):101.
8. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A. Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34(2):374-378.
9. http://base.thep.lu.se/:BASE Project Site. [http://base.thep.lu.se/.
10. Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G: The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 2005, 33(Database issue):D580-2.
11. Theilhaber J, Ulyanov A, Malanthara A, Cole J, Xu D, Nahf R, Heuer M, Brockel C, Bushnell S: GECKO: a complete large-scale gene expression analysis platform. BMC Bioinformatics 2004, 5(1):195.
12. https://genes.med.virginia.edu: GEOSS Home Page. [http:// genes.med.virginia.edu].
13. http://www.sbeams.org/: Systems Biology Experiment Analysis Management System. [http://www.sbeams.org/].
14. http://java.sun.com: Java Technology. [http://java.sun.com].
15. http://www.sbeams.org/Microarray: SBEAMS - Microarray. [http:// www.sbeams.org/Microarray].
16. http://subversion.tigris.org: subversion.tigris.org. [http:// subversion.tigris.org].
17. http://www.affymetrix.com: Affymetrix. [http://www.affymetrix.com].
18. Hubbell E, Liu WM, Mei R: Robust estimators for expression analysis. Bioinformatics 2002, 18(12):1585-1592.
19. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264.
20. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, lacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80.
21. Wu Z, Irizarry RA, Gentleman R, Murillo FM, Spencer F: A Model Based Background Adjustment for Oligonucleotide Expression Arrays. In Johns Hopkins University, Dept of Biostatistics Working Papers Baltimore, MD; 2004.
22. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18 Suppl 1:596-104.
23. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001, 98(1):31-36.
24. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193.
25. Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB, Saxild HH, Nielsen C, Brunak S, Knudsen S: A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3(9):research0048.
26. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98(9):5116-5121.
27. Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T: Tools enabling the elucidation of molecular pathways active in human disease:application to Hepatitis C virus infection. BMC Bioinformatics 2005, 6(1):154.
28. Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T: Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res 2004, 14(3):380-390.
29. 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 CJJ, Brazma A: Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 2002, 3(9):RESEARCH0046.
30. 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(1):68-71.
31. Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M: Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 2005, 21(8):466-475.