Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Huber, W.
Right arrow Articles by Vingron, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Huber, W.
Right arrow Articles by Vingron, M.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 90001 2002
Pages S96-S104
© 2002 Oxford University Press

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

Wolfgang Huber 1, Anja von Heydebreck 2, Holger Sültmann 1, Annemarie Poustka 1 and Martin Vingron 2

1 Department of Molecular Genome Analysis, German Cancer Research Center, INF 280, Heidelberg, 69120, Germany
2 Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Dahlem, Berlin, 14195, Germany

Received on January 24, 2002 ; revised on March 30, 2002 ; accepted on March 30, 2002

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In particular, we derive a transformation h for intensity measurements, and a difference statistic {Delta}h whose variance is approximately constant along the whole intensity range. This forms a basis for statistical inference from microarray data, and provides a rational data pre-processing strategy for multivariate analyses. For the transformation h, the parametric form h(x)=arsinh(a+bx) is derived from a model of the variance-versus-mean dependence for microarray intensity data, using the method of variance stabilizing transformations. For large intensities, h coincides with the logarithmic transformation, and {Delta}h with the log-ratio. The parameters of h together with those of the calibration between experiments are estimated with a robust variant of maximum-likelihood estimation. We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays.

Availability: Software is freely available for academic use as an R package at http://www.dkfz.de/abt0840/whuber

Contact: w.huber{at}dkfz.de


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
BioinformaticsHome page
D. Risso, M. S. Massa, M. Chiogna, and C. Romualdi
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
Bioinformatics, October 15, 2009; 25(20): 2685 - 2691.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. ProteomicsHome page
K. Kultima, A. Nilsson, B. Scholz, U. L. Rossbach, M. Falth, and P. E. Andren
Development and Evaluation of Normalization Methods for Label-free Relative Quantification of Endogenous Peptides
Mol. Cell. Proteomics, October 1, 2009; 8(10): 2285 - 2295.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
G. V. Glazko and F. Emmert-Streib
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets
Bioinformatics, September 15, 2009; 25(18): 2348 - 2354.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. ProteomicsHome page
D. M. Schlatzer, J.-E. Dazard, M. Dharsee, R. M. Ewing, S. Ilchenko, I. Stewart, G. Christ, and M. R. Chance
Urinary Protein Profiles in a Rat Model for Diabetic Complications
Mol. Cell. Proteomics, September 1, 2009; 8(9): 2145 - 2158.
[Abstract] [Full Text] [PDF]


Home page
Plant CellHome page
C.-W. Lee, M. Efetova, J. C Engelmann, R. Kramell, C. Wasternack, J. Ludwig-Muller, R. Hedrich, and R. Deeken
Agrobacterium tumefaciens Promotes Tumor Induction by Modulating Pathogen Defense in Arabidopsis thaliana
PLANT CELL, September 1, 2009; 21(9): 2948 - 2962.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
G.-J. Huang, S. Shifman, W. Valdar, M. Johannesson, B. Yalcin, M. S. Taylor, J. M. Taylor, R. Mott, and J. Flint
High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
Genome Res., June 1, 2009; 19(6): 1133 - 1140.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
P. Geeleher, D. Morris, J. P. Hinde, and A. Golden
BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server
Bioinformatics, June 1, 2009; 25(11): 1438 - 1439.
[Abstract] [Full Text] [PDF]


Home page
J. Virol.Home page
H. Hannemann, K. Rosenke, J. M. O'Dowd, and E. A. Fortunato
The Presence of p53 Influences the Expression of Multiple Human Cytomegalovirus Genes at Early Times Postinfection
J. Virol., May 1, 2009; 83(9): 4316 - 4325.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
M. Avissar, B. C. Christensen, K. T. Kelsey, and C. J. Marsit
MicroRNA Expression Ratio Is Predictive of Head and Neck Squamous Cell Carcinoma
Clin. Cancer Res., April 15, 2009; 15(8): 2850 - 2855.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
S. Bauersachs, S. E. Ulbrich, V. Zakhartchenko, M. Minten, M. Reichenbach, H.-D. Reichenbach, H. Blum, T. E. Spencer, and E. Wolf
The endometrium responds differently to cloned versus fertilized embryos
PNAS, April 7, 2009; 106(14): 5681 - 5686.
[Abstract] [Full Text] [PDF]


Home page
J. Cell Sci.Home page
J. H. Pomerantz, S. Mukherjee, A. T. Palermo, and H. M. Blau
Reprogramming to a muscle fate by fusion recapitulates differentiation
J. Cell Sci., April 1, 2009; 122(7): 1045 - 1053.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
T. Benoukraf, P. Cauchy, R. Fenouil, A. Jeanniard, F. Koch, S. Jaeger, D. Thieffry, J. Imbert, J.-C. Andrau, S. Spicuglia, et al.
CoCAS: a ChIP-on-chip analysis suite
Bioinformatics, April 1, 2009; 25(7): 954 - 955.
[Abstract] [Full Text] [PDF]


Home page
Cancer Genomics ProteomicsHome page
F. E. AHMED, P. W. VOS, C. JEFFRIES, J. E. WILEY, D. A. WEIDNER, H. MOTA, C. BONNERUP, C. SIBATA, and R. R. ALLISON
Differences in mRNA and microRNA Microarray Expression Profiles in Human Colon Adenocarcinoma HT-29 Cells Treated with either Intensity-modulated Radiation Therapy (IMRT), or Conventional Radiation Therapy (RT)
Cancer Genomics Proteomics, March 1, 2009; 6(2): 109 - 127.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
S. Pradervand, J. Weber, J. Thomas, M. Bueno, P. Wirapati, K. Lefort, G. P. Dotto, and K. Harshman
Impact of normalization on miRNA microarray expression profiling
RNA, March 1, 2009; 15(3): 493 - 501.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
X. Liu, L. F. Sempere, F. Galimberti, S. J. Freemantle, C. Black, K. H. Dragnev, Y. Ma, S. Fiering, V. Memoli, H. Li, et al.
Uncovering Growth-Suppressive MicroRNAs in Lung Cancer
Clin. Cancer Res., February 15, 2009; 15(4): 1177 - 1183.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, et al.
Quality Assessment and Data Analysis for microRNA Expression Arrays
Nucleic Acids Res., February 1, 2009; 37(2): e17 - e17.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. Biol.Home page
M. Terao, M. Kurosaki, M. M. Barzago, M. Fratelli, R. Bagnati, A. Bastone, C. Giudice, E. Scanziani, A. Mancuso, C. Tiveron, et al.
Role of the Molybdoflavoenzyme Aldehyde Oxidase Homolog 2 in the Biosynthesis of Retinoic Acid: Generation and Characterization of a Knockout Mouse
Mol. Cell. Biol., January 15, 2009; 29(2): 357 - 377.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
C. G. Knight, M. Platt, W. Rowe, D. C. Wedge, F. Khan, P. J. R. Day, A. McShea, J. Knowles, and D. B. Kell
Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
Nucleic Acids Res., January 1, 2009; 37(1): e6 - e6.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
O. Hartmann, F. Spyratos, N. Harbeck, D. Dietrich, A. Fassbender, M. Schmitt, S. Eppenberger-Castori, V. Vuaroqueaux, F. Lerebours, K. Welzel, et al.
DNA Methylation Markers Predict Outcome in Node-Positive, Estrogen Receptor-Positive Breast Cancer with Adjuvant Anthracycline-Based Chemotherapy
Clin. Cancer Res., January 1, 2009; 15(1): 315 - 323.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
R. Dai, R. A. Phillips, Y. Zhang, D. Khan, O. Crasta, and S. A. Ahmed
Suppression of LPS-induced Interferon-{gamma} and nitric oxide in splenic lymphocytes by select estrogen-regulated microRNAs: a novel mechanism of immune modulation
Blood, December 1, 2008; 112(12): 4591 - 4597.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
H. Frohlich, M. Fellmann, H. Sultmann, A. Poustka, and T. Beissbarth
Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data
Bioinformatics, November 15, 2008; 24(22): 2650 - 2656.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
K. H. Metzeler, M. Hummel, C. D. Bloomfield, K. Spiekermann, J. Braess, M.-C. Sauerland, A. Heinecke, M. Radmacher, G. Marcucci, S. P. Whitman, et al.
An 86-probe-set gene-expression signature predicts survival in cytogenetically normal acute myeloid leukemia
Blood, November 15, 2008; 112(10): 4193 - 4201.
[Abstract] [Full Text] [PDF]


Home page
GeneticsHome page
R. Chaix, M. Somel, D. P. Kreil, P. Khaitovich, and G. A. Lunter
Evolution of Primate Gene Expression: Drift and Corrective Sweeps?
Genetics, November 1, 2008; 180(3): 1379 - 1389.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. Biol.Home page
S. A. Mikolajczak, H. Silva-Rivera, X. Peng, A. S. Tarun, N. Camargo, V. Jacobs-Lorena, T. M. Daly, L. W. Bergman, P. de la Vega, J. Williams, et al.
Distinct Malaria Parasite Sporozoites Reveal Transcriptional Changes That Cause Differential Tissue Infection Competence in the Mosquito Vector and Mammalian Host
Mol. Cell. Biol., October 15, 2008; 28(20): 6196 - 6207.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
A. Oberthuer, L. Kaderali, Y. Kahlert, B. Hero, F. Westermann, F. Berthold, B. Brors, R. Eils, and M. Fischer
Subclassification and Individual Survival Time Prediction from Gene Expression Data of Neuroblastoma Patients by Using CASPAR
Clin. Cancer Res., October 15, 2008; 14(20): 6590 - 6601.
[Abstract] [Full Text] [PDF]


Home page
IOVSHome page
W. van Gils, E. M. Lodder, H. W. Mensink, E. Kilic, N. C. Naus, H. T. Bruggenwirth, W. van IJcken, D. Paridaens, G. P. Luyten, and A. de Klein
Gene Expression Profiling in Uveal Melanoma: Two Regions on 3p Related to Prognosis
Invest. Ophthalmol. Vis. Sci., October 1, 2008; 49(10): 4254 - 4262.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. ProteomicsHome page
S. F. Kingsmore, N. Kennedy, H. L. Halliday, J. C. Van Velkinburgh, S. Zhong, V. Gabriel, J. Grant, W. D. Beavis, V. T. Tchernev, L. Perlee, et al.
Identification of Diagnostic Biomarkers for Infection in Premature Neonates
Mol. Cell. Proteomics, October 1, 2008; 7(10): 1863 - 1875.
[Abstract] [Full Text] [PDF]


Home page
JEMHome page
V. Brune, E. Tiacci, I. Pfeil, C. Doring, S. Eckerle, C. J.M. van Noesel, W. Klapper, B. Falini, A. von Heydebreck, D. Metzler, et al.
Origin and pathogenesis of nodular lymphocyte-predominant Hodgkin lymphoma as revealed by global gene expression analysis
J. Exp. Med., September 29, 2008; 205(10): 2251 - 2268.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
J. W. Shin, R. Huggenberger, and M. Detmar
Transcriptional profiling of VEGF-A and VEGF-C target genes in lymphatic endothelium reveals endothelial-specific molecule-1 as a novel mediator of lymphangiogenesis
Blood, September 15, 2008; 112(6): 2318 - 2326.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
I. G. Costa, S. Roepcke, C. Hafemeister, and A. Schliep
Inferring differentiation pathways from gene expression
Bioinformatics, July 1, 2008; 24(13): i156 - i164.
[Abstract] [Full Text] [PDF]


Home page
Physiol. GenomicsHome page
R. Kuner, A. S. Barth, M. Ruschhaupt, A. Buness, L. Zwermann, E. Kreuzer, G. Steinbeck, A. Poustka, H. Sultmann, and M. Nabauer
Genomic analysis reveals poor separation of human cardiomyopathies of ischemic and nonischemic etiologies
Physiol Genomics, June 1, 2008; 34(1): 88 - 94.
[Abstract] [Full Text] [PDF]


Home page
haematolHome page
J. Dierlamm, E. M. Murga Penas, S. Bentink, S. Wessendorf, H. Berger, M. Hummel, W. Klapper, D. Lenze, A. Rosenwald, E. Haralambieva, et al.
Gain of chromosome region 18q21 including the MALT1 gene is associated with the activated B-cell-like gene expression subtype and increased BCL2 gene dosage and protein expression in diffuse large B-cell lymphoma
Haematologica, May 1, 2008; 93(5): 688 - 696.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
P. Van Vlierberghe, M. van Grotel, J. Tchinda, C. Lee, H. B. Beverloo, P. J. van der Spek, A. Stubbs, J. Cools, K. Nagata, M. Fornerod, et al.
The recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia
Blood, May 1, 2008; 111(9): 4668 - 4680.
[Abstract] [Full Text] [PDF]


Home page
Plant CellHome page
E. Lopez-Juez, E. Dillon, Z. Magyar, S. Khan, S. Hazeldine, S. M. de Jager, J. A.H. Murray, G. T.S. Beemster, L. Bogre, and H. Shanahan
Distinct Light-Initiated Gene Expression and Cell Cycle Programs in the Shoot Apex and Cotyledons of Arabidopsis
PLANT CELL, April 1, 2008; 20(4): 947 - 968.
[Abstract] [Full Text] [PDF]


Home page
JEMHome page
K. Petropoulos, N. Arseni, C. Schessl, C. R. Stadler, V. P.S. Rawat, A. J. Deshpande, B. Heilmeier, W. Hiddemann, L. Quintanilla-Martinez, S. K. Bohlander, et al.
A novel role for Lef-1, a central transcription mediator of Wnt signaling, in leukemogenesis
J. Exp. Med., March 17, 2008; 205(3): 515 - 522.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
M. Bak, A. Silahtaroglu, M. Moller, M. Christensen, M. F. Rath, B. Skryabin, N. Tommerup, and S. Kauppinen
MicroRNA expression in the adult mouse central nervous system
RNA, March 1, 2008; 14(3): 432 - 444.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
S. M. Lin, P. Du, W. Huber, and W. A. Kibbe
Model-based variance-stabilizing transformation for Illumina microarray data
Nucleic Acids Res., February 2, 2008; 36(2): e11 - e11.
[Abstract] [Full Text] [PDF]


Home page
ReproductionHome page
K. Mitko, S. E Ulbrich, H. Wenigerkind, F. Sinowatz, H. Blum, E. Wolf, and S. Bauersachs
Dynamic changes in messenger RNA profiles of bovine endometrium during the oestrous cycle
Reproduction, February 1, 2008; 135(2): 225 - 240.
[Abstract] [Full Text] [PDF]


Home page
Neuro Oncol DukeHome page
J. M. de Bont, J. M. Kros, M. M.C.J. Passier, R. E. Reddingius, P. A.E. S. Smitt, T. M. Luider, M. L. d. Boer, and R. Pieters
Differential expression and prognostic significance of SOX genes in pediatric medulloblastoma and ependymoma identified by microarray analysis
Neuro-oncol, January 1, 2008; 10(5): 648 - 660.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
R. Kelley, H. Feizi, and T. Ideker
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood
Bioinformatics, January 1, 2008; 24(1): 71 - 77.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
V. P. S. Rawat, S. Thoene, V. M. Naidu, N. Arseni, B. Heilmeier, K. Metzeler, K. Petropoulos, A. Deshpande, L. Quintanilla-Martinez, S. K. Bohlander, et al.
Overexpression of CDX2 perturbs HOX gene expression in murine progenitors depending on its N-terminal domain and is closely correlated with deregulated HOX gene expression in human acute myeloid leukemia
Blood, January 1, 2008; 111(1): 309 - 319.
[Abstract] [Full Text] [PDF]


Home page
Cancer Res.Home page
L. F. Sempere, M. Christensen, A. Silahtaroglu, M. Bak, C. V. Heath, G. Schwartz, W. Wells, S. Kauppinen, and C. N. Cole
Altered MicroRNA Expression Confined to Specific Epithelial Cell Subpopulations in Breast Cancer
Cancer Res., December 15, 2007; 67(24): 11612 - 11620.
[Abstract] [Full Text] [PDF]


Home page
IOVSHome page
D. M. Hornan, S. N. Peirson, A. J. Hardcastle, R. S. Molday, M. E. Cheetham, and A. R. Webster
Novel Retinal and Cone Photoreceptor Transcripts Revealed by Human Macular Expression Profiling
Invest. Ophthalmol. Vis. Sci., December 1, 2007; 48(12): 5388 - 5396.
[Abstract] [Full Text] [PDF]


Home page
Antimicrob. Agents Chemother.Home page
M. D. Brazas, E. B. M. Breidenstein, J. Overhage, and R. E. W. Hancock
Role of Lon, an ATP-Dependent Protease Homolog, in Resistance of Pseudomonas aeruginosa to Ciprofloxacin
Antimicrob. Agents Chemother., December 1, 2007; 51(12): 4276 - 4283.
[Abstract] [Full Text] [PDF]


Home page
Mol Hum ReprodHome page
Q. Pan, X. Luo, T. Toloubeydokhti, and N. Chegini
The expression profile of micro-RNA in endometrium and endometriosis and the influence of ovarian steroids on their expression
Mol. Hum. Reprod., November 1, 2007; 13(11): 797 - 806.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
M. E. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama, A. Holloway, and G. K. Smyth
A comparison of background correction methods for two-colour microarrays
Bioinformatics, October 15, 2007; 23(20): 2700 - 2707.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
M. Thomassen, Q. Tan, F. Eiriksdottir, M. Bak, S. Cold, and T. A. Kruse
Comparison of Gene Sets for Expression Profiling: Prediction of Metastasis from Low-Malignant Breast Cancer
Clin. Cancer Res., September 15, 2007; 13(18): 5355 - 5360.
[Abstract] [Full Text] [PDF]


Home page
J Exp BotHome page
J. G. Dubouzet, A. Ishihara, F. Matsuda, H. Miyagawa, H. Iwata, and K. Wakasa
Integrated metabolomic and transcriptomic analyses of high-tryptophan rice expressing a mutant anthranilate synthase alpha subunit
J. Exp. Bot., September 4, 2007; (2007) erm179v1.
[Abstract] [Full Text] [PDF]


Home page
J DAIRY SCIHome page
S. Bauersachs, K. Mitko, H. Blum, and E. Wolf
Technical Note: Bovine Oviduct and Endometrium Array Version 1: A Tailored Tool for Studying Bovine Endometrium Biology and Pathophysiology
J Dairy Sci, September 1, 2007; 90(9): 4420 - 4423.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
F. Westermann, K.-O. Henrich, J. S. Wei, W. Lutz, M. Fischer, R. Konig, R. Wiedemeyer, V. Ehemann, B. Brors, K. Ernestus, et al.
High Skp2 Expression Characterizes High-Risk Neuroblastomas Independent of MYCN Status
Clin. Cancer Res., August 15, 2007; 13(16): 4695 - 4703.
[Abstract] [Full Text] [PDF]


Home page
CirculationHome page
T. Thum, P. Galuppo, C. Wolf, J. Fiedler, S. Kneitz, L. W. van Laake, P. A. Doevendans, C. L. Mummery, J. Borlak, A. Haverich, et al.
MicroRNAs in the Human Heart: A Clue to Fetal Gene Reprogramming in Heart Failure
Circulation, July 17, 2007; 116(3): 258 - 267.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
S. Sundaresh, A. Randall, B. Unal, J. M. Petersen, J. T. Belisle, M. Gill Hartley, M. Duffield, R. W. Titball, D. H. Davies, P. L. Felgner, et al.
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis
Bioinformatics, July 1, 2007; 23(13): i508 - i518.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
J. L. Schultze and D. Eggle
IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform
Bioinformatics, June 1, 2007; 23(11): 1431 - 1433.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Chuchana, D. Marchand, M. Nugoli, C. Rodriguez, N. Molinari, and J. A. Garcia-Sanz
An adaptation of the LMS method to determine expression variations in profiling data
Nucleic Acids Res., May 14, 2007; 35(9): e71 - e71.
[Abstract] [Full Text] [PDF]


Home page
J. Exp. Biol.Home page
J. Quackenbush
Extracting biology from high-dimensional biological data
J. Exp. Biol., May 1, 2007; 210(9): 1507 - 1517.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
W. J. E. Tissing, M. L. den Boer, J. P. P. Meijerink, R. X. Menezes, S. Swagemakers, P. J. van der Spek, S. E. Sallan, S. A. Armstrong, and R. Pieters
Genomewide identification of prednisolone-responsive genes in acute lymphoblastic leukemia cells
Blood, May 1, 2007; 109(9): 3929 - 3935.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
R. Davey, G. Savva, J. Dicks, and I. N. Roberts
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets
Bioinformatics, April 15, 2007; 23(8): 1023 - 1025.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
S. Nacu, R. Critchley-Thorne, P. Lee, and S. Holmes
Gene expression network analysis and applications to immunology
Bioinformatics, April 1, 2007; 23(7): 850 - 858.
[Abstract] [Full Text] [PDF]


Home page
Hum Mol GenetHome page
A. F. McRae, N. A. Matigian, L. Vadlamudi, J. C. Mulley, B. Mowry, N. G. Martin, S. F. Berkovic, N. K. Hayward, and P. M. Visscher
Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines
Hum. Mol. Genet., February 15, 2007; 16(4): 364 - 373.
[Abstract] [Full Text] [PDF]


Home page
J Exp BotHome page
M. Friedmann, S. G. Ralph, D. Aeschliman, J. Zhuang, K. Ritland, B. E. Ellis, J. Bohlmann, and C. J. Douglas
Microarray gene expression profiling of developmental transitions in Sitka spruce (Picea sitchensis) apical shoots
J. Exp. Bot., February 1, 2007; 58(3): 593 - 614.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
J. Jaeger, D. Koczan, H.-J. Thiesen, S. M. Ibrahim, G. Gross, R. Spang, and M. Kunz
Gene Expression Signatures for Tumor Progression, Tumor Subtype, and Tumor Thickness in Laser-Microdissected Melanoma Tissues
Clin. Cancer Res., February 1, 2007; 13(3): 806 - 815.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
K. Lo and R. Gottardo
Flexible empirical Bayes models for differential gene expression
Bioinformatics, February 1, 2007; 23(3): 328 - 335.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
D. S. Yuan and R. A. Irizarry
High-resolution spatial normalization for microarrays containing embedded technical replicates
Bioinformatics, December 15, 2006; 22(24): 3054 - 3060.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
M. J. Vogel, L. Guelen, E. de Wit, D. P. Hupkes, M. Loden, W. Talhout, M. Feenstra, B. Abbas, A.-K. Classen, and B. van Steensel
Human heterochromatin proteins form large domains containing KRAB-ZNF genes
Genome Res., December 1, 2006; 16(12): 1493 - 1504.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
S. Yoon, Y. Yang, J. Choi, and J. Seong
Large scale data mining approach for gene-specific standardization of microarray gene expression data
Bioinformatics, December 1, 2006; 22(23): 2898 - 2904.
[Abstract] [Full Text] [PDF]


Home page
Plant CellHome page
R. Deeken, J. C. Engelmann, M. Efetova, T. Czirjak, T. Muller, W. M. Kaiser, O. Tietz, M. Krischke, M. J. Mueller, K. Palme, et al.
An Integrated View of Gene Expression and Solute Profiles of Arabidopsis Tumors: A Genome-Wide Approach
PLANT CELL, December 1, 2006; 18(12): 3617 - 3634.
[Abstract] [Full Text] [PDF]


Home page
Cancer Res.Home page
C. J. Marsit, K. Eddy, and K. T. Kelsey
MicroRNA Responses to Cellular Stress.
Cancer Res., November 15, 2006; 66(22): 10843 - 10848.
[Abstract] [Full Text] [PDF]


Home page
JCOHome page
A. Oberthuer, F. Berthold, P. Warnat, B. Hero, Y. Kahlert, R. Spitz, K. Ernestus, R. Konig, S. Haas, R. Eils, et al.
Customized Oligonucleotide Microarray Gene Expression-Based Classification of Neuroblastoma Patients Outperforms Current Clinical Risk Stratification
J. Clin. Oncol., November 1, 2006; 24(31): 5070 - 5078.
[Abstract] [Full Text] [PDF]


Home page
Toxicol SciHome page
H.-Q. Yin, M. Kim, J.-H. Kim, G. Kong, M.-O. Lee, K.-S. Kang, B.-I. Yoon, H.-L. Kim, and B.-H. Lee
Hepatic Gene Expression Profiling and Lipid Homeostasis in Mice Exposed to Steatogenic Drug, Tetracycline
Toxicol. Sci., November 1, 2006; 94(1): 206 - 216.
[Abstract] [Full Text] [PDF]


Home page
J Am Coll CardiolHome page
A. S. Barth, R. Kuner, A. Buness, M. Ruschhaupt, S. Merk, L. Zwermann, S. Kaab, E. Kreuzer, G. Steinbeck, U. Mansmann, et al.
Identification of a Common Gene Expression Signature in Dilated Cardiomyopathy Across Independent Microarray Studies
J. Am. Coll. Cardiol., October 17, 2006; 48(8): 1610 - 1617.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
E. S. Motakis, G. P. Nason, P. Fryzlewicz, and G. A. Rutter
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
Bioinformatics, October 15, 2006; 22(20): 2547 - 2553.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
T. Manoli, N. Gretz, H.-J. Grone, M. Kenzelmann, R. Eils, and B. Brors
Group testing for pathway analysis improves comparability of different microarray datasets
Bioinformatics, October 15, 2006; 22(20): 2500 - 2506.
[Abstract] [Full Text] [PDF]


Home page
JCOHome page
C. Roldo, E. Missiaglia, J. P. Hagan, M. Falconi, P. Capelli, S. Bersani, G. A. Calin, S. Volinia, C.-G. Liu, A. Scarpa, et al.
MicroRNA Expression Abnormalities in Pancreatic Endocrine and Acinar Tumors Are Associated With Distinctive Pathologic Features and Clinical Behavior
J. Clin. Oncol., October 10, 2006; 24(29): 4677 - 4684.
[Abstract] [Full Text] [PDF]


Home page
Toxicol SciHome page
L. N. Moens, K. van der Ven, P. Van Remortel, J. Del-Favero, and W. M. De Coen
Expression Profiling of Endocrine-Disrupting Compounds Using a Customized Cyprinus carpio cDNA Microarray
Toxicol. Sci., October 1, 2006; 93(2): 298 - 310.
[Abstract] [Full Text] [PDF]


Home page
HypertensionHome page
J. J. Saris, P. A.C. 't Hoen, I. M. Garrelds, D. H.W. Dekkers, J. T. den Dunnen, J. M.J. Lamers, and A.H. Jan Danser
Prorenin Induces Intracellular Signaling in Cardiomyocytes Independently of Angiotensin II
Hypertension, October 1, 2006; 48(4): 564 - 571.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
A. Papana and H. Ishwaran
CART variance stabilization and regularization for high-throughput genomic data
Bioinformatics, September 15, 2006; 22(18): 2254 - 2261.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
W. Huber, J. Toedling, and L. M. Steinmetz
Transcript mapping with high-density oligonucleotide tiling arrays
Bioinformatics, August 15, 2006; 22(16): 1963 - 1970.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
R. Kirschner-Schwabe, C. Lottaz, J. Todling, P. Rhein, L. Karawajew, C. Eckert, A. von Stackelberg, U. Ungethum, D. Kostka, A. E. Kulozik, et al.
Expression of Late Cell Cycle Genes and an Increased Proliferative Capacity Characterize Very Early Relapse of Childhood Acute Lymphoblastic Leukemia
Clin. Cancer Res., August 1, 2006; 12(15): 4553 - 4561.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
S. Sundaresh, D. L. Doolan, S. Hirst, Y. Mu, B. Unal, D. H. Davies, P. L. Felgner, and P. Baldi
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
Bioinformatics, July 15, 2006; 22(14): 1760 - 1766.
[Abstract] [Full Text] [PDF]


Home page
NEJMHome page
M. Hummel, S. Bentink, H. Berger, W. Klapper, S. Wessendorf, T. F.E. Barth, H.-W. Bernd, S. B. Cogliatti, J. Dierlamm, A. C. Feller, et al.
A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling.
N. Engl. J. Med., June 8, 2006; 354(23): 2419 - 2430.
[Abstract] [Full Text] [PDF]


Home page
Brief BioinformHome page
C. Steinhoff and M. Vingron
Normalization and quantification of differential expression in gene expression microarrays
Brief Bioinform, June 1, 2006; 7(2): 166 - 177.
[Abstract] [Full Text] [PDF]


Home page
Physiol. GenomicsHome page
M. Bauer, J. D. Katzenberger, A. C. Hamm, M. Bonaus, I. Zinke, J. Jaekel, and M. J. Pankratz
Purine and folate metabolism as a potential target of sex-specific nutrient allocation in Drosophila and its implication for lifespan-reproduction tradeoff
Physiol Genomics, May 16, 2006; 25(3): 393 - 404.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
K. Engelen, B. Naudts, B. De Moor, and K. Marchal
A calibration method for estimating absolute expression levels from microarray data
Bioinformatics, May 15, 2006; 22(10): 1251 - 1258.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
L. David, W. Huber, M. Granovskaia, J. Toedling, C. J. Palm, L. Bofkin, T. Jones, R. W. Davis, and L. M. Steinmetz
A high-resolution map of transcription in the yeast genome
PNAS, April 4, 2006; 103(14): 5320 - 5325.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
R. A. Irizarry, Z. Wu, and H. A. Jaffee
Comparison of Affymetrix GeneChip expression measures
Bioinformatics, April 1, 2006; 22(7): 789 - 794.
[Abstract] [Full Text] [PDF]


Home page
Brief BioinformHome page
M. Rattray, X. Liu, G. Sanguinetti, M. Milo, and N. D. Lawrence
Propagating uncertainty in microarray data analysis
Brief Bioinform, March 1, 2006; 7(1): 37 - 47.



Home page
Cancer Res.Home page
J. Cardoso, L. Molenaar, R. X. de Menezes, M. van Leerdam, C. Rosenberg, G. Moslein, J. Sampson, H. Morreau, J. M. Boer, and R. Fodde
Chromosomal Instability in MYH- and APC-Mutant Adenomatous Polyps.
Cancer Res., March 1, 2006; 66(5): 2514 - 2519.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
O. Shai, Q. D. Morris, B. J. Blencowe, and B. J. Frey
Inferring global levels of alternative splicing isoforms using a generative model of microarray data
Bioinformatics, March 1, 2006; 22(5): 606 - 613.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
D. de Ridder, F. J. T. Staal, J. J. M. van Dongen, and M. J. T. Reinders
Maximum significance clustering of oligonucleotide microarrays
Bioinformatics, February 1, 2006; 22(3): 326 - 331.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
M. R. Khondoker, C. A. Glasbey, and B. J. Worton
Statistical estimation of gene expression using multiple laser scans of microarrays
Bioinformatics, January 15, 2006; 22(2): 215 - 219.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
K.-O. Henrich, M. Fischer, D. Mertens, A. Benner, R. Wiedemeyer, B. Brors, A. Oberthuer, F. Berthold, J. S. Wei, J. Khan, et al.
Reduced Expression of CAMTA1 Correlates with Adverse Outcome in Neuroblastoma Patients
Clin. Cancer Res., January 1, 2006; 12(1): 131 - 138.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
H. M. Fathallah-Shaykh
Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays
Bioinformatics, December 1, 2005; 21(23): 4255 - 4262.
[Abstract] [Full Text] [PDF]



Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.