BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
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* Corresponding author: Carsten Peterson carsten@thep.lu.se
Genome Biology 2002, 3:software0003-software0003.6 doi:10.1186/gb-2002-3-8-software0003
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BioMed Central: 45 citations
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Research article
An Expression Map for Anopheles gambiae Robert M MacCallum, Seth N Redmond, George K Christophides BMC Genomics 2011, 12:620 (20 December 2011) |
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Research article
Breast tumors from CHEK2 1100delC-mutation carriers: genomic landscape and clinical implications Taru A Muranen, Dario Greco, Rainer Fagerholm, Outi Kilpivaara, Kati Kämpjärvi, Kristiina Aittomäki, Carl Blomqvist, Päivi Heikkilä, Åke Borg, Heli Nevanlinna Breast Cancer Research 2011, 13:R90 (20 September 2011) |
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Research article
Detecting microRNA activity from gene expression data Stephen F Madden, Susan B Carpenter, Ian B Jeffery, Harry Björkbacka, Katherine A Fitzgerald, Luke A O'Neill, Desmond G Higgins BMC Bioinformatics 2010, 11:257 (18 May 2010) |
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Software
Morris A Swertz, K Joeri Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, Ritsert C Jansen Genome Biology 2010, 11:R27 (9 March 2010) XGAP, a software platform for the integration and analysis of genotype and phenotype data. |
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Software
Gernot Stocker, Maria Fischer, Dietmar Rieder, Gabriela Bindea, Simon Kainz, Michael Oberstolz, James G McNally, Zlatko Trajanoski BMC Bioinformatics 2009, 10:390 (26 November 2009) |
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Research article
Potential predictive markers of chemotherapy resistance in stage III ovarian serous carcinomas Lovisa Österberg, Kristina Levan, Karolina Partheen, Ulla Delle, Björn Olsson, Karin Sundfeldt, György Horvath BMC Cancer 2009, 9:368 (18 October 2009) |
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Primary research
Sandra Karlsson, Björn Olsson, Karin Klinga-Levan Cancer Cell International 2009, 9:12 (8 May 2009) |
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Database
Adriane Menßen, Götz Edinger, Joachim R Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, Gerd-R Burmester, Thomas Häupl BMC Genomics 2009, 10:98 (5 March 2009) |
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Research article
Julien Gouré, Wendy A Findlay, Vincent Deslandes, Anne Bouevitch, Simon J Foote, Janet I MacInnes, James W Coulton, John HE Nash, Mario Jacques BMC Genomics 2009, 10:88 (24 February 2009) |
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Software
EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann BMC Bioinformatics 2009, 10:50 (6 February 2009) |
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Research article
Nirmala Sharma, Maureen Anderson, Arvind Kumar, Yan Zhang, E Michael Giblin, Suzanne R Abrams, L Irina Zaharia, David C Taylor, Pierre R Fobert BMC Genomics 2008, 9:619 (19 December 2008) |
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Software
Patrick J Killion, Vishwanath R Iyer Genome Biology 2008, 9:R159 (12 November 2008) ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics. |
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Database
MiMiR – an integrated platform for microarray data sharing, mining and analysis Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman, Laurence Game BMC Bioinformatics 2008, 9:379 (18 September 2008) |
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Research article
Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer Elin Karlsson, Ulla Delle, Anna Danielsson, Björn Olsson, Frida Abel, Per Karlsson, Khalil Helou BMC Cancer 2008, 8:254 (8 September 2008) |
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Research article
Eduardo N Taboada, Joanne M MacKinnon, Christian C Luebbert, Victor PJ Gannon, John HE Nash, Kris Rahn BMC Evolutionary Biology 2008, 8:229 (8 August 2008) |
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Research article
Sara Brommesson, Göran Jönsson, Carina Strand, Dorthe Grabau, Per Malmström, Markus Ringnér, Mårten Fernö, Ingrid Hedenfalk BMC Clinical Pathology 2008, 8:6 (10 July 2008) |
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Research article
Recurrent and multiple bladder tumors show conserved expression profiles David Lindgren, Sigurdur Gudjonsson, Kowan Jee, Fredrik Liedberg, Sonja Aits, Anna Andersson, Gunilla Chebil, Åke Borg, Sakari Knuutila, Thoas Fioretos, Wiking Månsson, Mattias Höglund BMC Cancer 2008, 8:183 (30 June 2008) Although recurrent urothelial tumors are unlikely to originate directly from the initial lesion, genome and transcriptome profiling suggests that the gene expression profile is established early in their development and maintained in subsequent tumors.
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Research article
The CD44+/CD24- phenotype is enriched in basal-like breast tumors Gabriella Honeth, Pär-Ola Bendahl, Markus Ringnér, Lao H Saal, Sofia K Gruvberger-Saal, Kristina Lövgren, Dorthe Grabau, Mårten Fernö, Åke Borg, Cecilia Hegardt Breast Cancer Research 2008, 10:R53 (17 June 2008) Basal-like and particularly BRCA1 hereditary breast cancer are associated with CD44+/CD24- cells, however tumorigenicity may not be confined to cells of this phenotype as they are found in very few HER2+ tumours.
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Method
Heidi Lyng, Malin Lando, Runar S Brøvig, Debbie H Svendsrud, Morten Johansen, Eivind Galteland, Odd T Brustugun, Leonardo A Meza-Zepeda, Ola Myklebost, Gunnar B Kristensen, Eivind Hovig, Trond Stokke Genome Biology 2008, 9:R86 (23 May 2008) GeneCount is a new method for exploring gene dosages and intratumor copy number heterogeneity in cancers from clinical array comparative genomic hybridization data.
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Database
RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina Ravi Kalathur, Nicolas Gagniere, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch BMC Genomics 2008, 9:208 (5 May 2008) |
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Research article
Prognostic Impact of Array-based Genomic Profiles in Esophageal Squamous Cell Cancer Ana Carneiro, Anna Isinger, Anna Karlsson, Jan Johansson, Göran Jönsson, Pär-Ola Bendahl, Dan Falkenback, Britta Halvarsson, Mef Nilbert BMC Cancer 2008, 8:98 (11 April 2008) |
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Methodology article
Tadeja Režen, Peter Juvan, Klementina Fon Tacer, Drago Kuzman, Adrian Roth, Denis Pompon, Lawrence P Aggerbeck, Urs A Meyer, Damjana Rozman BMC Genomics 2008, 9:76 (11 February 2008) |
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Methodology article
Normalization of array-CGH data: influence of copy number imbalances Johan Staaf, Göran Jönsson, Markus Ringnér, Johan Vallon-Christersson BMC Genomics 2007, 8:382 (22 October 2007) |
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Research
Responses of hyperthermophilic crenarchaea to UV irradiation Dorothee Götz, Sonia Paytubi, Stacey Munro, Magnus Lundgren, Rolf Bernander, Malcolm F White Genome Biology 2007, 8:R220 (11 October 2007) The transcriptional response to UV irradiation was analyzed in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius, showing a clear response to DNA damage but no increase in the expression of DNA repair genes. |
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Research article
Eduardo N Taboada, Alex van Belkum, Nobuhiro Yuki, Rey R Acedillo, Peggy CR Godschalk, Michiaki Koga, Hubert P Endtz, Michel Gilbert, John HE Nash BMC Genomics 2007, 8:359 (5 October 2007) |
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Database
The PhenoGen Informatics website: tools for analyses of complex traits Sanjiv V Bhave, Cheryl Hornbaker, Tzu L Phang, Laura Saba, Razvan Lapadat, Katherina Kechris, Jeanette Gaydos, Daniel McGoldrick, Andrew Dolbey, Sonia Leach, Brian Soriano, Allison Ellington, Eric Ellington, Kendra Jones, Jonathan Mangion, John K Belknap, Robert W Williams, Lawrence E Hunter, Paula L Hoffman, Boris Tabakoff BMC Genetics 2007, 8:59 (30 August 2007) PhenoGen Informatics, a new online database, provides access to new tools that can be used to store, integrate and analyze high-throughput data efficiently, including microarray, QTL, genotype and phenotype data for complex traits.
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Research article
Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray Johan Vallon-Christersson, Johan Staaf, Anders Kvist, Patrik Medstrand, Åke Borg, Carlos Rovira BMC Genomics 2007, 8:295 (29 August 2007) |
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Research
L Mariela Serrano, Douwe Molenaar, Michiel Wels, Bas Teusink, Peter A Bron, Willem M de Vos, Eddy J Smid Microbial Cell Factories 2007, 6:29 (28 August 2007) |
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Methodology article
Carina Strand, Johan Enell, Ingrid Hedenfalk, Mårten Fernö BMC Molecular Biology 2007, 8:38 (22 May 2007) |
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Research article
Princy Francis, Heidi Namløs, Christoph Müller, Patrik Edén, Josefin Fernebro, Jeanne-Marie Berner, Bodil Bjerkehagen, Måns Åkerman, Pär-Ola Bendahl, Anna Isinger, Anders Rydholm, Ola Myklebost, Mef Nilbert BMC Genomics 2007, 8:73 (14 March 2007) |
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Research
The Genopolis Microarray Database Andrea Splendiani, Marco Brandizi, Gael Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi-Castagnoli BMC Bioinformatics 2007, 8(Suppl 1):S21 (8 March 2007) |
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Research article
Mervi Jumppanen, Sofia Gruvberger-Saal, Päivikki Kauraniemi, Minna Tanner, Pär-Ola Bendahl, Mikael Lundin, Morten Krogh, Pasi Kataja, Åke Borg, Mårten Fernö, Jorma Isola Breast Cancer Research 2007, 9:R16 (31 January 2007) |
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Software
GeneTools – application for functional annotation and statistical hypothesis testing Vidar Beisvag, Frode KR Jünge, Hallgeir Bergum, Lars Jølsum, Stian Lydersen, Clara-Cecilie Günther, Heri Ramampiaro, Mette Langaas, Arne K Sandvik, Astrid Lægreid BMC Bioinformatics 2006, 7:470 (24 October 2006) |
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Software
Paul Honoré, Samuel Granjeaud, Rebecca Tagett, Stéphane Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono, Pascal Hingamp BMC Genomics 2006, 7:240 (20 September 2006) |
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Research article
Improving missing value imputation of microarray data by using spot quality weights Peter Johansson, Jari Häkkinen BMC Bioinformatics 2006, 7:306 (16 June 2006) Measuring microarray spot quality continuously, rather than with a binary measure that records poor-quality spots below a certain cutoff as absent, greatly improves the accuracy of missing value imputation.
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Research article
Evaluation of microarray data normalization procedures using spike-in experiments Patrik Rydén, Henrik Andersson, Mattias Landfors, Linda Näslund, Blanka Hartmanová, Laila Noppa, Anders Sjöstedt BMC Bioinformatics 2006, 7:300 (14 June 2006) |
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Software
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology Bruz Marzolf, Eric W Deutsch, Patrick Moss, David Campbell, Michael H Johnson, Timothy Galitski BMC Bioinformatics 2006, 7:286 (6 June 2006) |
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Database
Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes, Michael Primig BMC Bioinformatics 2006, 7:190 (5 April 2006) |
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Research
Comparative profiling of the sense and antisense transcriptome of maize lines Jiong Ma, Darren J Morrow, John Fernandes, Virginia Walbot Genome Biology 2006, 7:R22 (13 March 2006) Comparative transcriptome profiling of inbred maize lines demonstrates remarkable similarities and a large number of antisense transcripts. |
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Research article
Comparative genomics profiling of clinical isolates of Aeromonas salmonicida using DNA microarrays John HE Nash, Wendy A Findlay, Christian C Luebbert, Oksana L Mykytczuk, Simon J Foote, Eduardo N Taboada, Catherine D Carrillo, Jessica M Boyd, Duncan J Colquhoun, Michael E Reith, Laura L Brown BMC Genomics 2006, 7:43 (7 March 2006) |
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Methodology article
Henrik Bengtsson, Ola Hössjer BMC Bioinformatics 2006, 7:100 (1 March 2006) |
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Software
David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A Joseph Wood, Karim Nashar, Douglas B Kell, Andy Brass BMC Bioinformatics 2005, 6:264 (3 November 2005) |
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Software
arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman, Jo Vandesompele BMC Bioinformatics 2005, 6:124 (23 May 2005) |
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Research article
Henrik Bengtsson, Göran Jönsson, Johan Vallon-Christersson BMC Bioinformatics 2004, 5:177 (12 November 2004) |
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Database
Patrick J Killion, Gavin Sherlock, Vishwanath R Iyer BMC Bioinformatics 2003, 4:32 (20 August 2003) The Longhorn Array Database, a fully open source version of the Stanford Microarray Database, should facilitate the storage and analysis of two-color microarray data.
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