Bioinformatics. 2009 Feb 15;25(4):541-2. Epub 2008 Dec 19.

SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy.

Gatti DM, Sypa M, Rusyn I, Wright FA, Barry WT.

Source

Department of Environmental Sciences & Engineering, Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA.

Abstract

SUMMARY: A large number of websites and applications perform significance testing for gene categories/pathways in microarray data. Many of these packages fail to account for expression correlation between transcripts, with a resultant inflation in Type I error. Array permutation and other resampling-based approaches have been proposed as solutions to this problem. SAFEGUI provides a user-friendly graphical interface for the assessment of categorical significance in microarray studies, while properly accounting for the effects of correlations among genes. SAFEGUI incorporates both permutation and more recently proposed bootstrap algorithms that are demonstrated to be more powerful in detecting differential expression across categories of genes. AVAILABILITY: http://cebc.unc.edu/software/.

PMID:: 19098030; [PubMed - indexed for MEDLINE]
PMCID:: PMC2642635

Free PMC Article

Images from this publication.See all images (1) Free text

Publication Types, MeSH Terms

Publication Types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Save items

Related citations in PubMed

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. [Bioinformatics. 2007]
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering.
Xiang Z, Qin ZS, He Y. Bioinformatics. 2007 Jul 15; 23(14):1843-5. Epub 2007 May 7.
limmaGUI: a graphical user interface for linear modeling of microarray data. [Bioinformatics. 2004]
limmaGUI: a graphical user interface for linear modeling of microarray data.
Wettenhall JM, Smyth GK. Bioinformatics. 2004 Dec 12; 20(18):3705-6. Epub 2004 Aug 5.
A web-based tool for principal component and significance analysis of microarray data. [Bioinformatics. 2005]
A web-based tool for principal component and significance analysis of microarray data.
Sharov AA, Dudekula DB, Ko MS. Bioinformatics. 2005 May 15; 21(10):2548-9. Epub 2005 Feb 25.
Review An overview of Spotfire for gene-expression studies. [Curr Protoc Bioinformatics. 2004]
Review An overview of Spotfire for gene-expression studies.
Kaushal D, Naeve CW. Curr Protoc Bioinformatics. 2004 Sep; Chapter 7:Unit 7.7.
Review Growing applications and advancements in microarray technology and analysis tools. [Cell Biochem Biophys. 2005]
Review Growing applications and advancements in microarray technology and analysis tools.
Peeters JK, Van der Spek PJ. Cell Biochem Biophys. 2005; 43(1):149-66.

See reviews... See all...

Cited by 1 PubMed Central article

Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive hepatocellular carcinoma. [Mol Cancer. 2010]
Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive hepatocellular carcinoma.
Tsuchiya M, Parker JS, Kono H, Matsuda M, Fujii H, Rusyn I. Mol Cancer. 2010 Apr 9; 9:74. Epub 2010 Apr 9.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

SAFEGUI: resampling-based tests of categorical significance in gene expression d...
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy.
Bioinformatics. 2009 Feb 15 ;25(4):541-2. Epub 2008 Dec 19 .

PubMed
Bcl-2 family proteins contribute to apoptotic resistance in lung cancer multicel...
Bcl-2 family proteins contribute to apoptotic resistance in lung cancer multicellular spheroids.
Am J Respir Cell Mol Biol. 2009 Jul ;41(1):14-23. Epub 2008 Dec 18 .

PubMed
Intrapulmonary delivery of XCL1-targeting small interfering RNA in mice chronica...
Intrapulmonary delivery of XCL1-targeting small interfering RNA in mice chronically infected with Mycobacterium tuberculosis.
Am J Respir Cell Mol Biol. 2009 Aug ;41(2):136-45. Epub 2008 Dec 18 .

PubMed
Patterns of use of an automated interactive personalized coaching program for sm...
Patterns of use of an automated interactive personalized coaching program for smoking cessation.
J Med Internet Res. 2008 Dec 17 ;10(5):e54.

PubMed
Generation of induced pluripotent stem cell lines from adult rat cells.
Generation of induced pluripotent stem cell lines from adult rat cells.
Cell Stem Cell. 2009 Jan 9 ;4(1):11-5. Epub 2008 Dec 18 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: