Genome Biology

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Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application

Cheng Li and Wing Hung Wong*

Genome Biology 2001, 2:research0032-research0032.11 doi:10.1186/gb-2001-2-8-research0032

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Research article   Open Access

Analysis of tanshinone IIA induced cellular apoptosis in leukemia cells by genome-wide expression profiling

Chang Liu, Jianqin Li, Liangjie Wang, Fuqun Wu, Linfang Huang, Yue Xu, Jieyu Ye, Bin Xiao, Fanyi Meng, Shilin Chen, Mo Yang BMC Complementary and Alternative Medicine 2012, 12:5 (16 January 2012)

Method   Open Access Highly Accessed

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz Genome Biology 2011, 12:R41 (28 April 2011)

Identification of genes affected by somatic copy number variations that drive human cancer growth.

Review   Open Access

A maternal low protein diet has pronounced effects on mitochondrial gene expression in offspring liver and skeletal muscle; protective effect of taurine

Ole Mortensen, Hanne Olsen, Lis Frandsen, Peter Nielsen, Finn Nielsen, Niels Grunnet, Bjørn Quistorff Journal of Biomedical Science 2010, 17(Suppl 1):S38 (24 August 2010)

Methodology article   Open Access Highly Accessed

Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements

Jakub Mieczkowski, Magdalena E Tyburczy, Michal Dabrowski, Piotr Pokarowski BMC Bioinformatics 2010, 11:104 (24 February 2010)

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Cellular processes of v-Src transformation revealed by gene profiling of primary cells - Implications for human cancer

Bart M Maślikowski, Benjamin D Néel, Ying Wu, Lizhen Wang, Natalie A Rodrigues, Germain Gillet, Pierre-André Bédard BMC Cancer 2010, 10:41 (12 February 2010)

Methodology article   Open Access

A white-box approach to microarray probe response characterization: the BaFL pipeline

Kevin J Thompson, Hrishikesh Deshmukh, Jeffrey L Solka, Jennifer W Weller BMC Bioinformatics 2009, 10:449 (29 December 2009)

Research article   Open Access

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)

Martin J Aryee, José A Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush BMC Bioinformatics 2009, 10:409 (10 December 2009)

Research article   Open Access

A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: Evidence for masculinization of the transcriptome

Clayton M Small, Ginger E Carney, Qianxing Mo, Marina Vannucci, Adam G Jones BMC Genomics 2009, 10:579 (3 December 2009)

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A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Herman MJ Sontrop, Perry D Moerland, René van den Ham, Marcel JT Reinders, Wim FJ Verhaegh BMC Bioinformatics 2009, 10:389 (26 November 2009)

Research article   Open Access

Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells

K Blomberg, Nicole Boucheron, Jessica M Lindvall, Liang Yu, Julia Raberger, Anna Berglöf, Wilfried Ellmeier, CI Edvard Smith BMC Genomics 2009, 10:233 (18 May 2009)

Methodology article   Open Access Highly Accessed

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

Steven P Wilder, Pamela J Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Gauguier BMC Genomics 2009, 10:63 (5 February 2009)

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Positive correlation between gene coexpression and positional clustering in the zebrafish genome

Yen Kaow Ng, Wei Wu, Louxin Zhang BMC Genomics 2009, 10:42 (22 January 2009)

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Reconstruction and functional analysis of altered molecular pathways in human atherosclerotic arteries

Stefano Cagnin, Michele Biscuola, Cristina Patuzzo, Elisabetta Trabetti, Alessandra Pasquali, Paolo Laveder, Giuseppe Faggian, Mauro Iafrancesco, Alessandro Mazzucco, Pier Franco Pignatti, Gerolamo Lanfranchi BMC Genomics 2009, 10:13 (9 January 2009)

Methodology article   Open Access

Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data

Carl R Pelz, Molly Kulesz-Martin, Grover Bagby, Rosalie C Sears BMC Bioinformatics 2008, 9:520 (4 December 2008)

Methodology article   Open Access

A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips

Marta Blangiardo, Sylvia Richardson BMC Bioinformatics 2008, 9:512 (1 December 2008)

Research article   Open Access

Duration of chronic inflammation alters gene expression in muscle from untreated girls with juvenile dermatomyositis

Yi-Wen Chen, Rongye Shi, Nicholas Geraci, Sheela Shrestha, Heather Gordish-Dressman, Lauren M Pachman BMC Immunology 2008, 9:43 (31 July 2008)

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Control over the morphology and segregation of Zebrafish germ cell granules during embryonic development

Markus J Strasser, Natalia C Mackenzie, Karin Dumstrei, La-Iad Nakkrasae, Jürg Stebler, Erez Raz BMC Developmental Biology 2008, 8:58 (28 May 2008)

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Expression profiling in transgenic FVB/N embryonic stem cells overexpressing STAT3

Paolo Cinelli, Elisa A Casanova, Syndi Uhlig, Priska Lochmatter, Takahiko Matsuda, Takashi Yokota, Thomas Rülicke, Birgit Ledermann, Kurt Bürki BMC Developmental Biology 2008, 8:57 (23 May 2008)

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In vivo gene expression profiling of human intestinal epithelial cells: analysis by laser microdissection of formalin fixed tissues

Michael D George, Jan Wehkamp, Robert J Kays, Christian M Leutenegger, Sadiah Sabir, Irina Grishina, Satya Dandekar, Charles L Bevins BMC Genomics 2008, 9:209 (5 May 2008)

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Major copy proportion analysis of tumor samples using SNP arrays

Cheng Li, Rameen Beroukhim, Barbara A Weir, Wendy Winckler, Levi A Garraway, William R Sellers, Matthew Meyerson BMC Bioinformatics 2008, 9:204 (21 April 2008)

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In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

Tineke Casneuf, Yves Van de Peer, Wolfgang Huber BMC Bioinformatics 2007, 8:461 (26 November 2007)

Database   Open Access Highly Accessed

Arabidopsis Gene Family Profiler (aGFP) – user-oriented transcriptomic database with easy-to-use graphic interface

Nikoleta Dupl'áková, David Reňák, Patrik Hovanec, Barbora Honysová, David Twell, David Honys BMC Plant Biology 2007, 7:39 (23 July 2007)

Methodology article   Open Access

Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state

Daniel YL Yap, David K Smith, Xue W Zhang, Jeffrey Hill BMC Genomics 2007, 8:210 (3 July 2007)

Method   Open Access

Correcting for sequence biases in present/absent calls

Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton Genome Biology 2007, 8:R125 (26 June 2007)

Correction of non-specific binding for both PM and MM probes using probe-sequence models can partially remove the probe-sequence bias in Affymetrix microarray experiments and result in better performance of the MAS 5.0 algorithm.

Methodology article   Open Access

Orthogonal projections to latent structures as a strategy for microarray data normalization

Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Stefan Jansson, Thomas Moritz, Johan Trygg BMC Bioinformatics 2007, 8:207 (18 June 2007)

Research article   Open Access

A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

Walter D Park, Mark D Stegall BMC Genomics 2007, 8:88 (30 March 2007)

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Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships

Alan R Dabney, John D Storey Genome Biology 2007, 8:R44 (28 March 2007)

eCADS is a new method for multiple array normalization of two-channel microarrays that takes into account general experimental designs and intensity-dependent relationships and allows for a more efficient dye-swap design that requires only one array per sample pair.

Research article   Open Access

Including probe-level uncertainty in model-based gene expression clustering

Xuejun Liu, Kevin K Lin, Bogi Andersen, Magnus Rattray BMC Bioinformatics 2007, 8:98 (21 March 2007)

Research article   Open Access

Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine

Dorothy E Grice, Ilkka Reenilä, Pekka T Männistö, Andrew I Brooks, George G Smith, Greg T Golden, Joseph D Buxbaum, Wade H Berrettini BMC Genomics 2007, 8:76 (16 March 2007)

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microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder

Diana O Perkins, Clark D Jeffries, L Fredrik Jarskog, J Michael Thomson, Keith Woods, Martin A Newman, Joel S Parker, Jianping Jin, Scott M Hammond Genome Biology 2007, 8:R27 (27 February 2007)

Transcriptional profiling reveals a possible association between schizophrenia and altered miRNA expression

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An environmental signature for 323 microbial genomes based on codon adaptation indices

Hanni Willenbrock, Carsten Friis, Agnieszka S Juncker, David W Ussery Genome Biology 2006, 7:R114 (7 December 2006)

The correlation of two methods for estimating codon adaptation indices applied to more than 300 bacterial species shows that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle

Methodology article   Open Access

A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

Simon Katz, Rafael A Irizarry, Xue Lin, Mark Tripputi, Mark W Porter BMC Bioinformatics 2006, 7:464 (23 October 2006)

Research   Open Access

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

Jaroslav P Novak, Seon-Young Kim, Jun Xu, Olga Modlich, David J Volsky, David Honys, Joan L Slonczewski, Douglas A Bell, Fred R Blattner, Eduardo Blumwald, Marjan Boerma, Manuel Cosio, Zoran Gatalica, Marian Hajduch, Juan Hidalgo, Roderick R McInnes, Merrill C Miller III, Milena Penkowa, Michael S Rolph, Jordan Sottosanto, Rene St-Arnaud, Michael J Szego, David Twell, Charles Wang Biology Direct 2006, 1:27 (7 September 2006)

Commentary   Open Access Highly Accessed

Probe set algorithms: is there a rational best bet?

Jinwook Seo, Eric P Hoffman BMC Bioinformatics 2006, 7:395 (30 August 2006)

Newer probe set algorithms can avoid false positives resulting from poor probe sets, but assumptions about background expression have such an impact that the 'best' algorithm will vary from experiment to experiment.

Research article   Open Access

Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes

Michal Korostynski, Dorota Kaminska-Chowaniec, Marcin Piechota, Ryszard Przewlocki BMC Genomics 2006, 7:146 (13 June 2006)

Methodology article   Open Access

Correction of scaling mismatches in oligonucleotide microarray data

Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard, Michael Hubank BMC Bioinformatics 2006, 7:251 (9 May 2006)

Methodology article   Open Access Highly Accessed

Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies

Zihua Hu, Gail R Willsky BMC Bioinformatics 2006, 7:12 (10 January 2006)

Research article   Open Access Highly Accessed

Evaluation of normalization methods for cDNA microarray data by k-NN classification

Wei Wu, Eric P Xing, Connie Myers, I Saira Mian, Mina J Bissell BMC Bioinformatics 2005, 6:191 (26 July 2005)

Of forty-one strategies for removing dye biases in microarray data that were tested by k-NN leave-one-out-validation, three two-step processes, which removed intensity-dependent bias and local spatial effects, reduced classification errors most consistently and effectively across all data sets.

Correspondence   Open Access Highly Accessed

Considerations when using the significance analysis of microarrays (SAM) algorithm

Ola Larsson, Claes Wahlestedt, James A Timmons BMC Bioinformatics 2005, 6:129 (29 May 2005)

Research article   Open Access

An adaptive method for cDNA microarray normalization

Yingdong Zhao, Ming-Chung Li, Richard Simon BMC Bioinformatics 2005, 6:28 (11 February 2005)

Research   Open Access Highly Accessed

Global gene expression in neuroendocrine tumors from patients with the MEN1 syndrome

William G Dilley, Somasundaram Kalyanaraman, Sulekha Verma, J Perren Cobb, Jason M Laramie, Terry C Lairmore Molecular Cancer 2005, 4:9 (3 February 2005)

Method   Open Access

Genomic analysis of early murine mammary gland development using novel probe-level algorithms

Stephen R Master, Alexander J Stoddard, L Charles Bailey, Tien-Chi Pan, Katherine D Dugan, Lewis A Chodosh Genome Biology 2005, 6:R20 (1 February 2005)

A novel algorithm (ChipStat) is presented for detecting gene-expression changes from Affymetrix microarray data. The method is used to identify changes in murine mammary development.

Research   Open Access

Can gene expression profiling predict survival for patients with squamous cell carcinoma of the lung?

Zhifu Sun, Ping Yang, Marie-Christine Aubry, Farhad Kosari, Chiaki Endo, Julian Molina, George Vasmatzis Molecular Cancer 2004, 3:35 (3 December 2004)

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Transcriptome analysis of haploid male gametophyte development in Arabidopsis

David Honys, David Twell Genome Biology 2004, 5:R85 (27 October 2004)

A transcriptome analysis of male gametophyte development in Arabidopsis uncovers distinct temporal classes of gene expression and opens the door to detailed studies of the regulatory pathways involved.

Research   Open Access

Function-informed transcriptome analysis of Drosophila renal tubule

Jing Wang, Laura Kean, Jingli Yang, Adrian K Allan, Shireen A Davies, Pawel Herzyk, Julian AT Dow Genome Biology 2004, 5:R69 (26 August 2004)

Analysis of the transcriptome of the Drosophila melanogaster Malpighian (renal) tubule gives a radically new view of the function of the tubule, emphasising solute transport rather than fluid secretion.

Methodology article   Open Access

Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays

Chao Lu BMC Bioinformatics 2004, 5:103 (29 July 2004)

Method   Open Access Highly Accessed

A high performance test of differential gene expression for oligonucleotide arrays

William J Lemon, Sandya Liyanarachchi, Ming You Genome Biology 2003, 4:R67 (10 September 2003)

A method, Logit-t, for normalization of microarray data and for finding significantly differentially expressed genes has been described.

Software   Open Access Highly Accessed

Clustering gene-expression data with repeated measurements

Ka Yeung, Mario Medvedovic, Roger E Bumgarner Genome Biology 2003, 4:R34 (25 April 2003)

Algorithms that take advantage of repeated measurements yield more accurate and more stable clusters.

Research   Open Access Highly Accessed

Systematic determination of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002)

This article is part of a collection on Release 3 of the...

As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.

Research   Open Access Highly Accessed

DNA array analysis of interleukin-2-regulated immediate/early genes

Carol Beadling, Kendall A Smith Medical Immunology 2002, 1:2 (18 November 2002)

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A new non-linear normalization method for reducing variability in DNA microarray experiments

Christopher Workman, Lars Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak, Steen Knudsen Genome Biology 2002, 3:research0048-research0048.16 (30 August 2002)

A simple and robust non-linear method is presented for normalization using array signal distribution analysis and cubic splines. Both the regression and spline-based methods described performed better than existing linear methods when assessed on the variability of replicate arrays

Research   Open Access Highly Accessed

Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis

Reinhard Hoffmann, Thomas Seidl, Martin Dugas Genome Biology 2002, 3:research0033-research0033.11 (14 June 2002)

A number of procedures for normalization and detection of differentially expressed genes have been proposed. Four different normalization methods and all possible combinations with three different statistical algorithms have been used for detection of differentially expressed genes on a dataset. The number of genes detected as differentially expressed differs by a factor of about three.

Research   Open Access

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays

Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2002, 3:research0018-research0018.11 (22 March 2002)

A statistical analysis of a large number of duplicate high-density oligonucleotide arrays experiments showed that the noise inherent in these investigations is characteristically dependent on intensity and can be well described in terms of local normalization of log-ratio distributions. Robust estimates of the local standard deviation of these distributions provide a simple and powerful way to assess significance in differential gene expression experiments.

Deposited research article   Free

Characterization of the expression ratio noise structure in high-density oligonucleotide arrays

Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2001, 3:preprint0001-preprint0001.24 (7 December 2001)

New scoring functions for expression ratios and associated quality measures provide a powerful method for assessing the significance of differential gene expression results from high-density oligonucleotide arrays, relative to the noise resulting from the enzymatic and hybridization steps.