Improving identification of differentially expressed genes in microarray studies using information from public databases

Genome Biology
Richard D Kim, P J Park

Abstract

We demonstrate that the process of identifying differentially expressed genes in microarray studies with small sample sizes can be substantially improved by extracting information from a large number of datasets accumulated in public databases. The improvement comes from more reliable estimates of gene-specific variances based on other datasets. For a two-group comparison with two arrays in each group, for example, the result of our method was comparable to that of a t-test analysis with five samples in each group or to that of a regularized t-test analysis with three samples in each group. Our results are further improved by weighting the results of our approach with the regularized t-test results in a hybrid method.

References

Aug 14, 1998·Molecular Cell·R J ChoR W Davis
Oct 23, 1998·Science·S ChuI Herskowitz
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
May 8, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A NewtonK W Tsui
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M K KerrG A Churchill
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Jun 28, 2002·Cancer Cell·Dinesh SinghWilliam R Sellers
Sep 10, 2002·Bioinformatics·Daehee HwangGregory Stephanopoulos
Sep 27, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Philippe BroëtFrançois Radvanyi
Nov 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Judith N HaslettLouis M Kunkel
Nov 9, 2002·Bioinformatics·Olga G TroyanskayaRuss B Altman
Jan 10, 2003·Nucleic Acids Research·Alvis BrazmaSusanna-Assunta Sansone
Jan 10, 2003·Nucleic Acids Research·Jeremy GollubGavin Sherlock
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alexander ZienThomas Lengauer
Sep 12, 2003·Bioinformatics·Paul PavlidisWilliam Stafford Noble
Oct 15, 2003·Biostatistics·Aniko SzaboAndrei Y Yakovlev
Jun 25, 2004·Nucleic Acids Research·Kei-Hoi CheungKenneth R Williams

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Citations

Dec 17, 2005·Nucleic Acids Research·Laura L EloTero Aittokallio
Nov 10, 2005·Journal of Bioinformatics and Computational Biology·Rainer Breitling, Pawel Herzyk
Nov 21, 2009·American Journal of Respiratory and Critical Care Medicine·Sunita SharmaScott T Weiss
Oct 18, 2007·PloS One·Martin H van VlietMarcel J T Reinders
Sep 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Lu TianPeter J Park
Aug 2, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Laura L EloTero Aittokallio
Nov 23, 2006·Xenobiotica; the Fate of Foreign Compounds in Biological Systems·L Hultin-RosenbergJ D Tugwood
Aug 8, 2007·The Plant Journal : for Cell and Molecular Biology·Anja WilleLars Hennig

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Methods Mentioned

BETA
chips
chip
reverse transcription PCR

Software Mentioned

SNOMAD
GEO
MAS

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