Gene-expression measurement: variance-modeling considerations for robust data analysis.

Shankar Subramaniam, Gene Hsiao
Author Information
  1. Shankar Subramaniam: Department of Bioengineering, University of California at San Diego, La Jolla, California, USA. shankar@ucsd.edu

Abstract

System-wide measurements of gene expression by DNA microarray and, more recently, RNA-sequencing strategies have become de facto tools of modern biology and have led to deep understanding of biological mechanisms and pathways. However, analyses of the measurements have often ignored statistically robust methods that account for variance, resulting in misleading biological interpretations.

References

  1. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18745-50 [PMID: 19841271]
  2. Bioinformatics. 2004 Nov 22;20(17):3108-27 [PMID: 15217816]
  3. Biostatistics. 2003 Apr;4(2):249-64 [PMID: 12925520]
  4. BMC Bioinformatics. 2010 May 27;11:285 [PMID: 20507584]
  5. PLoS One. 2010 Sep 03;5(9):e12336 [PMID: 20838429]
  6. Nat Rev Immunol. 2009 Oct;9(10):741-7 [PMID: 19763148]
  7. Nat Rev Genet. 2006 Jan;7(1):55-65 [PMID: 16369572]
  8. Bioinformatics. 2001 Jun;17(6):509-19 [PMID: 11395427]
  9. Nat Methods. 2008 Jul;5(7):621-8 [PMID: 18516045]
  10. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 [PMID: 11309499]
  11. Stat Appl Genet Mol Biol. 2004;3:Article3 [PMID: 16646809]
  12. Nat Rev Mol Cell Biol. 2005 Feb;6(2):99-111 [PMID: 15654321]
  13. Nat Rev Microbiol. 2005 Apr;3(4):281-94 [PMID: 15806094]
  14. Syst Synth Biol. 2008 Dec;2(3-4):95-104 [PMID: 19680790]
  15. Genome Res. 2008 Sep;18(9):1509-17 [PMID: 18550803]
  16. Genome Biol. 2010;11(10):R106 [PMID: 20979621]

Grants

  1. R38 AI140299/NIAID NIH HHS
  2. U19 AI090023/NIAID NIH HHS
  3. P01 DK074868/NIDDK NIH HHS
  4. U54 GM069338/NIGMS NIH HHS
  5. R33 HL087375/NHLBI NIH HHS

MeSH Term

Analysis of Variance
Animals
Gene Expression
Humans
Models, Immunological
Sequence Analysis, RNA

Word Cloud

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