Literature DB >> 24244802

Identification of significant features in DNA microarray data.

Eric Bair1.   

Abstract

DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA microarray experiments is to identify genes associated with biological processes of interest. Conventional statistical tests often produce poor results when applied to microarray data owing to small sample sizes, noisy data, and correlation among the expression levels of the genes. Thus, novel statistical methods are needed to identify significant genes in DNA microarray experiments. This article discusses the challenges inherent in DNA microarray analysis and describes a series of statistical techniques that can be used to overcome these challenges. The problem of multiple hypothesis testing and its relation to microarray studies are also considered, along with several possible solutions.

Entities:  

Keywords:  feature selection; genetics; microarray; multiple testing

Year:  2013        PMID: 24244802      PMCID: PMC3826574          DOI: 10.1002/wics.1260

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Comput Stat        ISSN: 1939-0068


  95 in total

1.  Interpretation, design, and analysis of gene array expression experiments.

Authors:  R A Miller; A Galecki; R J Shmookler-Reis
Journal:  J Gerontol A Biol Sci Med Sci       Date:  2001-02       Impact factor: 6.053

2.  Global gene expression profiling in Escherichia coli K12. The effects of integration host factor.

Authors:  S M Arfin; A D Long; E T Ito; L Tolleri; M M Riehle; E S Paegle; G W Hatfield
Journal:  J Biol Chem       Date:  2000-09-22       Impact factor: 5.157

3.  CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts.

Authors:  E P Xing; R M Karp
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

4.  A model for measurement error for gene expression arrays.

Authors:  D M Rocke; B Durbin
Journal:  J Comput Biol       Date:  2001       Impact factor: 1.479

Review 5.  Microarray data analysis: from disarray to consolidation and consensus.

Authors:  David B Allison; Xiangqin Cui; Grier P Page; Mahyar Sabripour
Journal:  Nat Rev Genet       Date:  2006-01       Impact factor: 53.242

6.  Variable selection for model-based high-dimensional clustering and its application to microarray data.

Authors:  Sijian Wang; Ji Zhu
Journal:  Biometrics       Date:  2007-10-26       Impact factor: 2.571

7.  Semi-supervised recursively partitioned mixture models for identifying cancer subtypes.

Authors:  Devin C Koestler; Carmen J Marsit; Brock C Christensen; Margaret R Karagas; Raphael Bueno; David J Sugarbaker; Karl T Kelsey; E Andres Houseman
Journal:  Bioinformatics       Date:  2010-08-16       Impact factor: 6.937

8.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

9.  TESTING SIGNIFICANCE OF FEATURES BY LASSOED PRINCIPAL COMPONENTS.

Authors:  Daniela M Witten; Robert Tibshirani
Journal:  Ann Appl Stat       Date:  2008-09-01       Impact factor: 2.083

10.  Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies.

Authors:  Ignacio Medina; David Montaner; Nuria Bonifaci; Miguel Angel Pujana; José Carbonell; Joaquin Tarraga; Fatima Al-Shahrour; Joaquin Dopazo
Journal:  Nucleic Acids Res       Date:  2009-06-05       Impact factor: 16.971

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  2 in total

1.  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

2.  An enhanced topologically significant directed random walk in cancer classification using gene expression datasets.

Authors:  Choon Sen Seah; Shahreen Kasim; Mohd Farhan Md Fudzee; Jeffrey Mark Law Tze Ping; Mohd Saberi Mohamad; Rd Rohmat Saedudin; Mohd Arfian Ismail
Journal:  Saudi J Biol Sci       Date:  2017-11-20       Impact factor: 4.219

  2 in total

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