Genome Biology

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Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells

Jae K Lee*, Kimberly J Bussey, Fuad G Gwadry, William Reinhold, Gregory Riddick, Sandra L Pelletier, Satoshi Nishizuka, Gergely Szakacs, Jean-Phillipe Annereau, Uma Shankavaram, Samir Lababidi, Lawrence H Smith, Michael M Gottesman and John N Weinstein*

Genome Biology 2003, 4:R82 doi:10.1186/gb-2003-4-12-r82

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Research   Open Access

TLX1 and NOTCH coregulate transcription in T cell acute lymphoblastic leukemia cells

Irene Riz, Teresa S Hawley, Truong V Luu, Norman H Lee, Robert G Hawley Molecular Cancer 2010, 9:181 (9 July 2010)

Research article   Open Access

Comparison and consolidation of microarray data sets of human tissue expression

Jenny Russ, Matthias E Futschik BMC Genomics 2010, 11:305 (14 May 2010)

Research article   Open Access Highly Accessed

Correlations between RNA and protein expression profiles in 23 human cell lines

Marcus Gry, Rebecca Rimini, Sara Strömberg, Anna Asplund, Fredrik Pontén, Mathias Uhlén, Peter Nilsson BMC Genomics 2009, 10:365 (7 August 2009)

Research article   Open Access Highly Accessed

Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions

Ki-Yeol Kim, Dong Ki, Hei-Cheul Jeung, Hyun Chung, Sun Rha BMC Bioinformatics 2008, 9:283 (16 June 2008)

Research   Open Access

On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation

Wing-Cheong Wong, Marie Loh, Frank Eisenhaber Biology Direct 2008, 3:23 (3 June 2008)

Method   Open Access Highly Accessed

Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data

Chang-Kyu Lee, Susan M Sunkin, Chihchau Kuan, Carol L Thompson, Sayan Pathak, Lydia Ng, Chris Lau, Shanna Fischer, Marty Mortrud, Cliff Slaughterbeck, Allan Jones, Ed Lein, Michael Hawrylycz Genome Biology 2008, 9:R23 (30 January 2008)

This study introduces a novel method for standardized relative quantification of colorimetric in situ hybridization signal that enables a large-scale cross-platform expression level comparison of in situ hybridization with two publicly available microarray brain data sources.

Research article   Open Access

Application of a correlation correction factor in a microarray cross-platform reproducibility study

Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T Garrett BMC Bioinformatics 2007, 8:447 (15 November 2007)

Methodology article   Open Access Highly Accessed

A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments

Hyungwon Choi, Ronglai Shen, Arul M Chinnaiyan, Debashis Ghosh BMC Bioinformatics 2007, 8:364 (27 September 2007)

Research article   Open Access

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

Zizhen Yao, Jochen C Jaeger, Walter L Ruzzo, Cecile Z Morale, Mary Emond, Uta Francke, Dianna M Milewicz, Stephen M Schwartz, Eileen R Mulvihill BMC Genomics 2007, 8:319 (12 September 2007)

Software   Open Access Highly Accessed

Strategy for encoding and comparison of gene expression signatures

Yajun Yi, Chun Li, Clay Miller, Alfred L George Genome Biology 2007, 8:R133 (5 July 2007)

EXALT (EXpression signature AnaLysis Tool) enables comparisons of microarray data across experimental platforms and different laboratories.

Research article   Open Access

Defining the gene expression signature of rhabdomyosarcoma by meta-analysis

Chiara Romualdi, Cristiano De Pittà, Lucia Tombolan, Stefania Bortoluzzi, Francesca Sartori, Angelo Rosolen, Gerolamo Lanfranchi BMC Genomics 2006, 7:287 (7 November 2006)

Research article   Open Access

An analysis of intra array repeats: the good, the bad and the non informative

Yedid Elbez, Shlomit Farkash-Amar, Itamar Simon BMC Genomics 2006, 7:136 (5 June 2006)

Database   Open Access Highly Accessed

An online database for brain disease research

Brandon W Higgs, Michael Elashoff, Sam Richman, Beata Barci BMC Genomics 2006, 7:70 (4 April 2006)

The Stanley Medical Research Institute online genomics database presents a web-based system for searching clinical and microarray data from studies into brain disorders such as schizophrenia, bipolar disorder and depression.

Methodology article   Open Access Highly Accessed

Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips

Fred van Ruissen, Jan M Ruijter, Gerben J Schaaf, Lida Asgharnegad, Danny A Zwijnenburg, Marcel Kool, Frank Baas BMC Genomics 2005, 6:91 (14 June 2005)

Research article   Open Access Highly Accessed

Three microarray platforms: an analysis of their concordance in profiling gene expression

David Petersen, GVR Chandramouli, Joel Geoghegan, Joanne Hilburn, Jonathon Paarlberg, Chang Kim, David Munroe, Lisa Gangi, Jing Han, Raj Puri, Lou Staudt, John Weinstein, J Carl Barrett, Jeffrey Green, Ernest S Kawasaki BMC Genomics 2005, 6:63 (5 May 2005)

Methodology article   Open Access Highly Accessed

Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements

Scott L Carter, Aron C Eklund, Brigham H Mecham, Isaac S Kohane, Zoltan Szallasi BMC Bioinformatics 2005, 6:107 (25 April 2005)

Commentary   Free

Microarrays and breast cancer clinical studies: forgetting what we have not yet learnt

Ahmed Ahmed, James D Brenton Breast Cancer Research 2005, 7:96-99 (1 April 2005)

Research   Open Access

HLA class I and II genotype of the NCI-60 cell lines

Sharon Adams, Fu-Meei Robbins, Deborah Chen, Devika Wagage, Susan L Holbeck, Herbert C Morse, David Stroncek, Francesco M Marincola Journal of Translational Medicine 2005, 3:11 (4 March 2005)

Research article   Open Access

Combining gene expression data from different generations of oligonucleotide arrays

Kyu-Baek Hwang, Sek Kong, Steve A Greenberg, Peter J Park BMC Bioinformatics 2004, 5:159 (25 October 2004)