Genome Biology

official impact factor 6.89

Highly Access

Statistical tests for differential expression in cDNA microarray experiments

Xiangqin Cui and Gary A Churchill*

Genome Biology 2003, 4:210 doi:10.1186/gb-2003-4-4-210

Accesses  

  • Last 30 days: 328 accesses
  • Last year: 3235 accesses
  • All time: 37349 accesses

Cited by

BioMed Central: 44 citations

Research article   Open Access

A searchable cross-platform gene expression database reveals connections between drug treatments and disease

Gareth Williams BMC Genomics 2012, 13:12 (10 January 2012)

Proceedings   Open Access

Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

Jia Meng, Jianqiu (Michelle) Zhang, Yidong Chen, Yufei Huang Proteome Science 2011, 9(Suppl 1):S9 (14 October 2011)

Database   Open Access

Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data

Gareth R Howell, David O Walton, Benjamin L King, Richard T Libby, Simon WM John BMC Genomics 2011, 12:429 (24 August 2011)

Research article   Open Access

Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes

Klaus Jung, Tim Friede, Tim Beißbarth BMC Bioinformatics 2011, 12:288 (15 July 2011)

Proceedings   Open Access

Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants

Alexander A Morgan, Purvesh Khatri, Richard Jones, Minnie M Sarwal, Atul J Butte BMC Bioinformatics 2010, 11(Suppl 9):S6 (28 October 2010)

Software   Open Access

ProbFAST: Probabilistic Functional Analysis System Tool

Israel T Silva, Ricardo ZN Vêncio, Thiago YK Oliveira, Greice A Molfetta, Wilson A Silva BMC Bioinformatics 2010, 11:161 (30 March 2010)

Methodology article   Open Access

An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

Erdem Arslan, Ian J Laurenzi BMC Bioinformatics 2009, 10:411 (10 December 2009)

Research article   Open Access Highly Accessed

Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family

Sandeep Sanga, Bradley M Broom, Vittorio Cristini, Mary E Edgerton BMC Medical Genomics 2009, 2:59 (11 September 2009)

Research   Open Access Highly Accessed

Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers

Jonathan M Dreyfuss, Mark D Johnson, Peter J Park Molecular Cancer 2009, 8:71 (4 September 2009)

Research article   Open Access Highly Accessed

The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma

Cinzia Di Pietro, Marco Ragusa, Davide Barbagallo, Laura R Duro, Maria R Guglielmino, Alessandra Majorana, Rosario Angelica, Marina Scalia, Luisa Statello, Loredana Salito, Luisa Tomasello, Salvo Pernagallo, Salvo Valenti, Vito D'Agostino, Patrizio Triberio, Igor Tandurella, Giuseppe A Palumbo, Piera La Cava, Viviana Cafiso, Taschia Bertuccio, Maria Santagati, Giovanni Li Destri, Salvatore Lanzafame, Francesco Di Raimondo, Stefania Stefani, Bud Mishra, Michele Purrello BMC Medical Genomics 2009, 2:20 (30 April 2009)

Methodology article   Open Access Highly Accessed

Comparison of small n statistical tests of differential expression applied to microarrays

Carl Murie, Owen Woody, Anna Y Lee, Robert Nadon BMC Bioinformatics 2009, 10:45 (3 February 2009)

Methodology article   Open Access

Bayesian optimal discovery procedure for simultaneous significance testing

Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, Michael A White BMC Bioinformatics 2009, 10:5 (6 January 2009)

Research   Open Access

Selecting informative genes for discriminant analysis using multigene expression profiles

Xin Yan, Tian Zheng BMC Genomics 2008, 9(Suppl 2):S14 (16 September 2008)

Research   Open Access

ILOOP – a web application for two-channel microarray interwoven loop design

Mehdi Pirooznia, Ping Gong, Jack Y Yang, Mary Yang, Edward J Perkins, Youping Deng BMC Genomics 2008, 9(Suppl 2):S11 (16 September 2008)

Methodology article   Open Access

Between-groups within-gene heterogeneity of residual variances in microarray gene expression data

Joaquim Casellas, Luis Varona BMC Genomics 2008, 9:319 (4 July 2008)

Research article   Open Access Highly Accessed

Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection

M Navajas, A Migeon, C Alaux, ML Martin-Magniette, GE Robinson, JD Evans, S Cros-Arteil, D Crauser, Y Le Conte BMC Genomics 2008, 9:301 (25 June 2008)

Methodology article   Open Access Highly Accessed

Extracting expression modules from perturbational gene expression compendia

Steven Maere, Patrick Van Dijck, Martin Kuiper BMC Systems Biology 2008, 2:33 (10 April 2008)

Research article   Open Access Highly Accessed

The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution

Kirstin Replogle, Arthur P Arnold, Gregory F Ball, Mark Band, Staffan Bensch, Eliot A Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M George, George Gong, Dennis Hasselquist, Alvaro G Hernandez, Ryan Kim, Harris A Lewin, Lei Liu, Peter V Lovell, Claudio V Mello, Sara Naurin, Sandra Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, David F Clayton BMC Genomics 2008, 9:131 (18 March 2008)

The Songbird Neurogenomics initiative (SoNG) provides a genomic database, a set of genomic tools and also a mechanism for community collaboration to enhance research linking the genomics, evolution, neuroscience and behavior of songbirds.

Methodology article   Open Access Highly Accessed

Ranking analysis of F-statistics for microarray data

Yuan-De Tan, Myriam Fornage, Hongyan Xu BMC Bioinformatics 2008, 9:142 (6 March 2008)

Research article   Open Access

Amplification biases: possible differences among deviating gene expressions

Séverine A Degrelle, Christelle Hennequet-Antier, Hélène Chiapello, Karine Piot-Kaminski, Francois Piumi, Stéphane Robin, Jean-Paul Renard, Isabelle Hue BMC Genomics 2008, 9:46 (28 January 2008)

Research article   Open Access

Evaluation of time profile reconstruction from complex two-color microarray designs

Ana C Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet BMC Bioinformatics 2008, 9:1 (3 January 2008)

Research article   Open Access Highly Accessed

Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium

Teresa M Bergholz, Lukas M Wick, Weihong Qi, James T Riordan, Lindsey M Ouellette, Thomas S Whittam BMC Microbiology 2007, 7:97 (29 October 2007)

Research   Open Access Highly Accessed

Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte

Amal J Johnston, Patrick Meier, Jacqueline Gheyselinck, Samuel EJ Wuest, Michael Federer, Edith Schlagenhauf, Jörg D Becker, Ueli Grossniklaus Genome Biology 2007, 8:R204 (3 October 2007)

Genetic subtraction and expression profiling of wild-type Arabidopsis and a sporophytic mutant lacking an embryo sac identified 1,260 genes expressed in the embryo sac; a total of 527 genes were identified for their expression in ovules of mutants lacking an embryo sac.

Research   Open Access

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1

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)

Software   Open Access Highly Accessed

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

Curtis Huttenhower, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya, Hilary A Coller BMC Bioinformatics 2007, 8:250 (12 July 2007)

Research article   Open Access

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees

Moushumi Sen Sarma, Charles W Whitfield, Gene E Robinson BMC Genomics 2007, 8:202 (29 June 2007)

Research   Open Access Highly Accessed

Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray

Xiaohong Zhang, Omar De la Cruz, Jayant M Pinto, Dan Nicolae, Stuart Firestein, Yoav Gilad Genome Biology 2007, 8:R86 (17 May 2007)

Using a microarray, expression of 76% of predicted human olfactory receptor genes was detected in olfactory epithelia, and many were expressed in non-olfactory tissues.

Poster presentation   Open Access

A global statistical test for improved detection of gene activity

David JG Bakewell, Ernst Wit BMC Systems Biology 2007, 1(Suppl 1):P10 (8 May 2007)

Research article   Open Access

A meta-data based method for DNA microarray imputation

Rebecka Jörnsten, Ming Ouyang, Hui-Yu Wang BMC Bioinformatics 2007, 8:109 (29 March 2007)

Method   Open Access Highly Accessed

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   Open Access

Significance analysis of microarray transcript levels in time series experiments

Barbara Di Camillo, Gianna Toffolo, Sreekumaran K Nair, Laura J Greenlund, Claudio Cobelli BMC Bioinformatics 2007, 8(Suppl 1):S10 (8 March 2007)

Research article   Open Access

Normalization of low-density microarray using external spike-in controls: analysis of macrophage cell lines expression profile

Paolo Fardin, Stefano Moretti, Barbara Biasotti, Annamaria Ricciardi, Stefano Bonassi, Luigi Varesio BMC Genomics 2007, 8:17 (17 January 2007)

Research   Open Access

The impact of sample imbalance on identifying differentially expressed genes

Kun Yang, Jianzhong Li, Hong Gao BMC Bioinformatics 2006, 7(Suppl 4):S8 (12 December 2006)

Research   Open Access

Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

Jaroslav P Novak, Merrill C Miller, Douglas A Bell Biology Direct 2006, 1:18 (20 June 2006)

Research article   Open Access

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

Allan A Sioson, Shrinivasrao P Mane, Pinghua Li, Wei Sha, Lenwood S Heath, Hans J Bohnert, Ruth Grene BMC Bioinformatics 2006, 7:215 (20 April 2006)

Research article   Open Access Highly Accessed

Construction and validation of a Bovine Innate Immune Microarray

Laurelea Donaldson, Tony Vuocolo, Christian Gray, Ylva Strandberg, Antonio Reverter, Sean McWilliam, YongHong Wang, Keren Byrne, Ross Tellam BMC Genomics 2005, 6:135 (22 September 2005)

Software   Open Access

Storing, linking, and mining microarray databases using SRS

Antoine Veldhoven, Don de Lange, Marcel Smid, Victor de Jager, Jan A Kors, Guido Jenster BMC Bioinformatics 2005, 6:192 (27 July 2005)

Methodology article   Open Access Highly Accessed

Validating internal controls for quantitative plant gene expression studies

Amy M Brunner, Igor A Yakovlev, Steven H Strauss BMC Plant Biology 2004, 4:14 (18 August 2004)

Methodology article   Open Access

Tests for finding complex patterns of differential expression in cancers: towards individualized medicine

James Lyons-Weiler, Satish Patel, Michael J Becich, Tony E Godfrey BMC Bioinformatics 2004, 5:110 (12 August 2004)

Methodology article   Open Access

Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray

Susan CP Renn, Nadia Aubin-Horth, Hans A Hofmann BMC Genomics 2004, 5:42 (6 July 2004)

Methodology article   Open Access Highly Accessed

Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments

Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:34 (29 March 2004)

Research article   Open Access

Incorporation of gene-specific variability improves expression analysis using high-density DNA microarrays

Vikram Budhraja, Edward Spitznagel, W Timothy Schaiff, Yoel Sadovsky BMC Biology 2003, 1:1 (28 November 2003)

A new method quantifies the extent to which microarray signal variability is dependent on the specific set of probes used. Taking this unrecognized source of variability into account can considerably improve the reliability of microarray analysis.

Software   Open Access Highly Accessed

Identifying biological themes within lists of genes with EASE

Douglas A Hosack, Glynn Dennis, Brad T Sherman, H Lane, Richard A Lempicki Genome Biology 2003, 4:R70 (11 September 2003)

EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data.