Microarray experiments and factors which affect their reliability

Biology Direct
Roman JaksikMarek Kimmel

Abstract

Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very complex, requiring sophisticated methods to control for various factors that are inherent to the procedures used. In this article we describe the individual steps of a microarray experiment, highlighting important elements and factors that may affect the processes involved and that influence the interpretation of the results. Additionally, we describe methods that can be used to estimate the influence of these factors, and to control the way in which they affect the expression estimates. A comprehensive understanding of the experimental protocol used in a microarray experiment aids the interpretation of the obtained results. By describing known factors which affect expression estimates this article provides guidelines for appropriate quality control and pre-processing of the data, additionally applicable to other transcriptome analysis methods that utilize similar sample handling protocols.

References

Jul 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·B Sauer, N Henderson
May 24, 1994·Proceedings of the National Academy of Sciences of the United States of America·A C PeaseS P Fodor
Feb 3, 1998·Nature Biotechnology·G Ramsay
Dec 1, 1996·Nature Biotechnology·D J LockhartE L Brown
Apr 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Douglas Kyung NamSan Ming Wang
May 7, 2003·Applied and Environmental Microbiology·Hidetoshi UrakawaDavid A Stahl
Sep 3, 2003·BMC Bioinformatics·Taesung ParkRichard Simon
Sep 27, 2003·Analytical Biochemistry·Bahram AreziHolly H Hogrefe
Nov 25, 2003·Analytical Chemistry·Thomas L FareYanqun Wang
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Feb 13, 2004·Bioinformatics·Leslie M CopeTerence P Speed
Jan 22, 2005·The Journal of Immunology : Official Journal of the American Association of Immunologists·Tatsuya SaitohShoji Yamaoka
Apr 23, 2005·Nature Methods·Rafael A IrizarryWayne Yu
Jun 15, 2005·Annual Review of Biochemistry·Roland B Stoughton
Dec 13, 2005·BMC Bioinformatics·Mayte Suárez-FariñasMarcelo O Magnasco
Dec 29, 2005·Trends in Genetics : TIG·Sorin DraghiciZoltan Szallasi
Jan 6, 2006·Environmental Health Perspectives·Johanna M BeekmanLaura Suter
Feb 2, 2006·BMC Molecular Biology·Andreas SchroederThomas Ragg
Feb 14, 2006·Bioinformatics·Sepp HochreiterKlaus Obermayer
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Jun 2, 2006·Nucleic Acids Research·Shimyn SlomovicGadi Schuster
Aug 29, 2006·Bioinformatics·Kellie J Archer, Tobias Guennel
Sep 12, 2006·Nature Biotechnology·Roger D CanalesFederico M Goodsaid
Sep 12, 2006·Nature Biotechnology·Weida TongLeming Shi
Jan 20, 2007·Omics : a Journal of Integrative Biology·Saran VardhanabhutiDilip Rajagopalan
Mar 3, 2007·Bioinformatics·Jun S SongX Shirley Liu
Mar 28, 2007·Bioinformatics·Thomas E RoyceMark B Gerstein
Apr 10, 2007·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Penelope M WebbAdèle C Green
Jun 15, 2007·Nucleic Acids Research·Dmitriy SkvortsovSimon Tavaré
Aug 19, 2007·Nucleic Acids Research·Stefano CalzaYudi Pawitan
Nov 17, 2007·BMC Bioinformatics·Francesco FerrariSilvio Bicciato

❮ Previous
Next ❯

Citations

Apr 19, 2017·International Journal of Molecular Sciences·Mariarosaria IncoronatoMarco Salvatore
Apr 17, 2018·Experimental Dermatology·Jacob SubashAmy McMichael
Oct 28, 2018·Bioscience Reports·Kyoung Hwa LeeSang Hoon Han
Jul 4, 2018·Molecular Systems Biology·Luca ParcaAlessandro Ori
Feb 26, 2020·Briefings in Bioinformatics·Daniel Toro-DomínguezPedro Carmona-Sáez
May 14, 2020·European Journal of Nuclear Medicine and Molecular Imaging·Min-Jeong KimRobert B Innis
Nov 11, 2020·Biological Research·Vasantha H S KumarLori Nielsen
Aug 20, 2019·Life Sciences in Space Research·Kianoosh PeyvanAndrew Pohorille
Jan 31, 2021·Scientific Reports·Pedro J Gutiérrez-DíezJose Russo
Mar 6, 2021·PloS One·Kyung Soo KimYonggoo Kim
Feb 20, 2021·Bioscience, Biotechnology, and Biochemistry·Montek BoparaiPaul C H Li
Mar 17, 2020·Computers in Biology and Medicine·Turki Turki, Y-H Taguchi
Oct 11, 2019·ACS Chemical Biology·Ryan P ConnellyYulia V Gerasimova

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
ChIP-chip
in vitro transcription
PCR
electrophoresis
chip

Software Mentioned

DAT
Affymetrix
CEL

Related Concepts

Related Feeds

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

Related Papers

Wiley Interdisciplinary Reviews. Computational Statistics
Eric Bair
Tidsskrift for den Norske lægeforening : tidsskrift for praktisk medicin, ny række
A K SandvikO Myklebost
Pediatric Clinics of North America
Martin J HessnerAnne E Kwitek
© 2021 Meta ULC. All rights reserved