Literature DB >> 22212230

Statistical considerations for analysis of microarray experiments.

Kouros Owzar1, William T Barry, Sin-Ho Jung.   

Abstract

Microarray technologies enable the simultaneous interrogation of expressions from thousands of genes from a biospecimen sample taken from a patient. This large set of expressions generates a genetic profile of the patient that may be used to identify potential prognostic or predictive genes or genetic models for clinical outcomes. The aim of this article is to provide a broad overview of some of the major statistical considerations for the design and analysis of microarrays experiments conducted as correlative science studies to clinical trials. An emphasis will be placed on how the lack of understanding and improper use of statistical concepts and methods will lead to noise discovery and misinterpretation of experimental results.
© 2011 Wiley Periodicals, Inc.

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Year:  2011        PMID: 22212230      PMCID: PMC3906917          DOI: 10.1111/j.1752-8062.2011.00309.x

Source DB:  PubMed          Journal:  Clin Transl Sci        ISSN: 1752-8054            Impact factor:   4.689


  29 in total

1.  Power and sample size for DNA microarray studies.

Authors:  Mei-Ling Ting Lee; G A Whitmore
Journal:  Stat Med       Date:  2002-12-15       Impact factor: 2.373

2.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors:  B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

3.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

Authors:  Rafael A Irizarry; Bridget Hobbs; Francois Collin; Yasmin D Beazer-Barclay; Kristen J Antonellis; Uwe Scherf; Terence P Speed
Journal:  Biostatistics       Date:  2003-04       Impact factor: 5.899

4.  Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments.

Authors:  Michael A Black; R W Doerge
Journal:  Bioinformatics       Date:  2002-12       Impact factor: 6.937

5.  A benchmark for Affymetrix GeneChip expression measures.

Authors:  Leslie M Cope; Rafael A Irizarry; Harris A Jaffee; Zhijin Wu; Terence P Speed
Journal:  Bioinformatics       Date:  2004-02-12       Impact factor: 6.937

6.  Statistical methods of background correction for Illumina BeadArray data.

Authors:  Yang Xie; Xinlei Wang; Michael Story
Journal:  Bioinformatics       Date:  2009-02-04       Impact factor: 6.937

7.  Gene expression profiling predicts clinical outcome of breast cancer.

Authors:  Laura J van 't Veer; Hongyue Dai; Marc J van de Vijver; Yudong D He; Augustinus A M Hart; Mao Mao; Hans L Peterse; Karin van der Kooy; Matthew J Marton; Anke T Witteveen; George J Schreiber; Ron M Kerkhoven; Chris Roberts; Peter S Linsley; René Bernards; Stephen H Friend
Journal:  Nature       Date:  2002-01-31       Impact factor: 49.962

8.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

9.  Gene-expression profiles predict survival of patients with lung adenocarcinoma.

Authors:  David G Beer; Sharon L R Kardia; Chiang-Ching Huang; Thomas J Giordano; Albert M Levin; David E Misek; Lin Lin; Guoan Chen; Tarek G Gharib; Dafydd G Thomas; Michelle L Lizyness; Rork Kuick; Satoru Hayasaka; Jeremy M G Taylor; Mark D Iannettoni; Mark B Orringer; Samir Hanash
Journal:  Nat Med       Date:  2002-07-15       Impact factor: 53.440

10.  PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.

Authors:  Vamsi K Mootha; Cecilia M Lindgren; Karl-Fredrik Eriksson; Aravind Subramanian; Smita Sihag; Joseph Lehar; Pere Puigserver; Emma Carlsson; Martin Ridderstråle; Esa Laurila; Nicholas Houstis; Mark J Daly; Nick Patterson; Jill P Mesirov; Todd R Golub; Pablo Tamayo; Bruce Spiegelman; Eric S Lander; Joel N Hirschhorn; David Altshuler; Leif C Groop
Journal:  Nat Genet       Date:  2003-07       Impact factor: 38.330

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  14 in total

1.  Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects.

Authors:  Anthony D Sung; Shekeab Jauhari; Sharareh Siamakpour-Reihani; Arati V Rao; Janet Staats; Cliburn Chan; Everett Meyer; Vijayakrishna K Gadi; Andrew B Nixon; Jing Lyu; Jichun Xie; Lauren Bohannon; Zhiguo Li; Christopher S Hourigan; Laura W Dillon; Hong Yuen Wong; Rebecca Shelby; Louis Diehl; Carlos de Castro; Thomas LeBlanc; Danielle Brander; Harry Erba; Ahmed Galal; Alexandra Stefanovic; Nelson Chao; David A Rizzieri
Journal:  Am J Hematol       Date:  2020-03-30       Impact factor: 10.047

2.  Genomic profiling in locally advanced and inflammatory breast cancer and its link to DCE-MRI and overall survival.

Authors:  Sharareh Siamakpour-Reihani; Kouros Owzar; Chen Jiang; Peter M Scarbrough; Oana I Craciunescu; Janet K Horton; Holly K Dressman; Kimberly L Blackwell; Mark W Dewhirst
Journal:  Int J Hyperthermia       Date:  2015-03-26       Impact factor: 3.914

3.  FAS Death Receptor: A Breast Cancer Subtype-Specific Radiation Response Biomarker and Potential Therapeutic Target.

Authors:  Janet K Horton; Sharareh Siamakpour-Reihani; Chen-Ting Lee; Ying Zhou; Wei Chen; Joseph Geradts; Diane R Fels; Peter Hoang; Kathleen A Ashcraft; Jeff Groth; Hsiu-Ni Kung; Mark W Dewhirst; Jen-Tsan A Chi
Journal:  Radiat Res       Date:  2015-10-21       Impact factor: 2.841

4.  Differential expression of immune related genes in high-grade ovarian serous carcinoma.

Authors:  Sharareh Siamakpour-Reihani; Lauren Patterson Cobb; Chen Jiang; Dadong Zhang; Rebecca A Previs; Kouros Owzar; Andrew B Nixon; Angeles Alvarez Secord
Journal:  Gynecol Oncol       Date:  2020-01-07       Impact factor: 5.482

5.  Prognostic significance of differential expression of angiogenic genes in women with high-grade serous ovarian carcinoma.

Authors:  Sharareh Siamakpour-Reihani; Kouros Owzar; Chen Jiang; Taylor Turner; Yiwen Deng; Sarah M Bean; Janet K Horton; Andrew Berchuck; Jeffrey R Marks; Mark W Dewhirst; Angeles Alvarez Secord
Journal:  Gynecol Oncol       Date:  2015-08-07       Impact factor: 5.482

6.  Combinatorial code governing cellular responses to complex stimuli.

Authors:  Antonio Cappuccio; Raphaël Zollinger; Mirjam Schenk; Aleksandra Walczak; Nicolas Servant; Emmanuel Barillot; Philippe Hupé; Robert L Modlin; Vassili Soumelis
Journal:  Nat Commun       Date:  2015-04-21       Impact factor: 14.919

7.  How to get the most from microarray data: advice from reverse genomics.

Authors:  Ivan P Gorlov; Ji-Yeon Yang; Jinyoung Byun; Christopher Logothetis; Olga Y Gorlova; Kim-Anh Do; Christopher Amos
Journal:  BMC Genomics       Date:  2014-03-21       Impact factor: 3.969

8.  A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size.

Authors:  Daniel Vasiliu; Samuel Clamons; Molly McDonough; Brian Rabe; Margaret Saha
Journal:  PLoS One       Date:  2015-03-04       Impact factor: 3.240

Review 9.  Statistical Issues in the Design and Analysis of nCounter Projects.

Authors:  Sin-Ho Jung; Insuk Sohn
Journal:  Cancer Inform       Date:  2014-12-14

10.  An Optimization-Driven Analysis Pipeline to Uncover Biomarkers and Signaling Paths: Cervix Cancer.

Authors:  Enery Lorenzo; Katia Camacho-Caceres; Alexander J Ropelewski; Juan Rosas; Michael Ortiz-Mojer; Lynn Perez-Marty; Juan Irizarry; Valerie Gonzalez; Jesús A Rodríguez; Mauricio Cabrera-Rios; Clara Isaza
Journal:  Microarrays (Basel)       Date:  2015-06
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