Statistical modeling of large microarray data sets to identify stimulus-response profiles

Proceedings of the National Academy of Sciences of the United States of America
L P ZhaoLinda L Breeden

Abstract

A statistical modeling approach is proposed for use in searching large microarray data sets for genes that have a transcriptional response to a stimulus. The approach is unrestricted with respect to the timing, magnitude or duration of the response, or the overall abundance of the transcript. The statistical model makes an accommodation for systematic heterogeneity in expression levels. Corresponding data analyses provide gene-specific information, and the approach provides a means for evaluating the statistical significance of such information. To illustrate this strategy we have derived a model to depict the profile expected for a periodically transcribed gene and used it to look for budding yeast transcripts that adhere to this profile. Using objective criteria, this method identifies 81% of the known periodic transcripts and 1,088 genes, which show significant periodicity in at least one of the three data sets analyzed. However, only one-quarter of these genes show significant oscillations in at least two data sets and can be classified as periodic with high confidence. The method provides estimates of the mean activation and deactivation times, induced and basal expression levels, and statistical measures of the precision ...Continue Reading

References

Oct 1, 1996·Proceedings of the National Academy of Sciences of the United States of America·M SchenaR W Davis
Jan 1, 1997·Methods in Enzymology·L L Breeden
May 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·R J ChoR W Davis
Aug 14, 1998·Molecular Cell·R J ChoR W Davis
Jan 23, 1999·Nature Genetics·E S Lander
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·P TamayoT R Golub
Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Mar 14, 2000·Current Opinion in Immunology·G Sherlock
Jul 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·N S HolterN V Fedoroff
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein

❮ Previous
Next ❯

Citations

Apr 19, 2002·Biochimica Et Biophysica Acta·Jerald P Radich
Jul 20, 2010·Nature·Takahiro ItoTannishtha Reya
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ziv Bar-JosephItamar Simon
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gal Chechik, Daphne Koller
Aug 24, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Bong-Rae KimArthur Berg
Apr 6, 2006·Omics : a Journal of Integrative Biology·Desheng HuangWei Pan
Jul 13, 2011·Briefings in Bioinformatics·Yaqun WangRongling Wu
Oct 30, 2004·Bioinformatics·Ulrik de LichtenbergSøren Brunak
Oct 14, 2005·Bioinformatics·Karen WillbrandThomas M A Fink
Oct 18, 2007·Nucleic Acids Research·Nicholas Paul GauthierThomas Skøt Jensen
Sep 15, 2006·Journal of the Royal Society, Interface·Francis J Doyle, Jörg Stelling
Aug 4, 2005·Journal of Bioinformatics and Computational Biology·Xu Guo, Wei Pan
Aug 2, 2008·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Chu ChenLue Ping Zhao
Aug 22, 2009·BMC Bioinformatics·Alain B TchagangPanayiotis V Benos
Feb 2, 2010·BMC Bioinformatics·Ritesh KrishnaVicky Buchanan-Wollaston
May 17, 2005·BMC Bioinformatics·Miika AhdesmäkiOlli Yli-Harja
Feb 14, 2006·BMC Bioinformatics·Claes R AnderssonMats G Gustafsson
Feb 16, 2005·BMC Genomics·Wenhong FanLue Ping Zhao
Oct 28, 2003·Cell & Chromosome·Stephen Cooper, Kerby Shedden
Jul 22, 2009·BMC Systems Biology·Frank Emmert-Streib, Matthias Dehmer
Jul 31, 2013·BMC Systems Biology·Chao ChengMark Gerstein
Aug 19, 2009·PloS One·Frank Emmert-Streib, Matthias Dehmer
Jan 19, 2012·PloS One·Daifeng WangMia K Markey
Jan 28, 2014·BMC Research Notes·Li-Xuan QinSteven G Self
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Delong LiuClarice R Weinberg
Sep 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Maga RowickaZbyszek Otwinowski
Aug 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ziv Bar-JosephTommi S Jaakkola
Oct 3, 2006·Expert Review of Molecular Diagnostics·Mar BellidoJerald P Radich
May 5, 2010·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Tracy L Bergemann

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.