References for “Microarray softwares review”
YUK FAI LEUNG
Department of Ophthalmology and Visual Sciences, Chinese University of Hong
Kong, 3/F Hong Kong Eye Hospital, 147K Argyle Street, Hong Kong
Tel: (852) 27623152 Fax: (852) 27159490
email: yfleung@cuhk.edu.hk, yfleung@genomicshome.com
URL: http://ihome.cuhk.edu.hk/~b400559 or http://genomicshome.com
Image analysis
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Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D. Fully automatic
quantification of microarray image data. Genome Res. 2002 Feb;12(2):325-32.
Yang YH, Buckley MJ, Speed TP. Analysis of cDNA microarray images.Brief Bioinform.
2001 Dec;2(4):341-9.
Brown CS, Goodwin PC, Sorger PK. Image metrics in the statistical analysis of DNA
microarray data. Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):8944-9.
Data mining
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Sherlock G. Analysis of large-scale gene expression data. Brief Bioinform. 2001
Dec;2(4):350-62.
Wu TD. Analysing gene expression data from DNA microarrays to identify candidate genes. J
Pathol. 2001 Sep;195(1):53-65.
Quackenbush J. Computational genetics computational analysis of microarray data. Nat Rev
Genet. 2001 Jun;2(6):418-27.
Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Basic microarray analysis: grouping and
feature reduction. Trends Biotechnol. 2001. May; 19:189-193
Brazma A, Vilo J.Gene expression data analysis. FEBS Lett. 2000 Aug 25;480(1):17-24.
Specific software
Cleaver
1. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Basic microarray analysis: grouping and
feature reduction. Trends Biotechnol. 2001. May; 19:189-193
Cluster & Treeview
1. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide
expression patterns. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8.
Cyber T
1. Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data:
regularized t -test and statistical inferences of gene changes. Bioinformatics. 2001
Jun;17(6):509-19.
Expression Profiler
1. Quackenbush J. Expression Profiler: A suite of web-based tools for the analysis of microarray
gene expression data. Brief Bioinform. 2001 Dec;2(4):388-392
GeneSpring
1. Aronow BJ. GeneSpring and GeNet. Brief Bioinform. 2001 Dec;2(4):397-402
GeneSight
1. Draghici S, Kuklin A, Hoff B, Shams S. Experimental design, analysis of variance and slide
quality assessment in gene expression arrays. Curr Opin Drug Dis Dev. 2001 May; 4:332-337.
Microarray Explorer
1. Taylor R, Leach S. The Microarray Explorer analysis package. Brief Bioinform. 2001
Dec;2(4):392-394
2. Lemkin PF, Thornwall GC, Walton KD, Hennighausen L.The microarray explorer tool for
data mining of cDNA microarrays: application for the mammary gland. Nucleic Acids Res.
2000 Nov 15;28(22):4452-9.
R/ S-plus
1. Krause A, Olson M. The Basics of S and S-Plus (Statistics and Computing) Springer Verlag
2000.
2. Venables WN, Ripley BD. Modern Applied Statistics With S-Plus (Statistics and Computing)
Springer Verlag 1999.
3. Selvin S. Modern Applied Biostatistical Methods: Using S-Plus. Oxford University Press.
1998
SAM (significance Analysis of Microarrays)
1. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing
radiation response. Proc. Natl Acad Sci. 2001 Apr 24;98(9):5116-21.
SMA package
1. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA
microarray data: a robust composite method addressing single and multiple slide systematic
variation. Nucleic Acids Res. 2002 Feb 15;30(4):E15.
2. Lonnstedt I, Speed TP. Replicated Microarray Data. Statistica Sinica 2002 Jan.
SNP analysis
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Tillib SV, Mirzabekov AD. Advances in the analysis of DNA sequence variations using
oligonucleotide microchip technology. Curr Opin Biotechnol. 2001 Feb;12(1):53-8.
Database
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Gardiner-Garden M, Littlejohn TG. A comparison of microarray databases. Brief Bioinform.
2001 May;2(2):143-58.
Public Database
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Miles MF. OPINION Microarrays: lost in a storm of data? Nat Rev Neurosci. 2001
Jun;2(6):441-3.
Becker KG. OPINION The sharing of cDNA microarray data. Nat Rev Neurosci. 2001
Jun;2(6):438-40.
Geschwind DH. OPINION Sharing gene expression data: an array of options. Nat Rev
Neurosci. 2001 Jun;2(6):435-8.
Gardiner-Garden M, Littlejohn TG. A comparison of microarray databases. Brief Bioinform.
2001 May;2(2):143-58.
ExpressDB
1. Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene
expression data. Genome Res. 2000 Apr;10(4):431-45.
GEO
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Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and
hybridization array data repository Nucleic Acids Res. 2002 Jan; 30: 207-210.
HuGE Index
1. Haverty PM, Weng Z, Best NL, Auerbach KR, Hsiao LL, Jensen RV, Gullans SR. HugeIndex:
a database with visualization tools for high-density oligonucleotide array data from normal
human tissues. Nucleic Acids Res. 2002 Jan; 30: 214-217.
READ
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SMD
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SGD
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yMGV
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Bono H, Kasukawa T, Hayashizaki Y, Okazaki Y. READ: RIKEN Expression Array Database.
Nucleic Acids Res. 2002 Jan; 30: 211-213.
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper
M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The
Stanford Microarray Database. Nucleic Acids Res. 2001 Jan 1;29(1):152-5.
Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver
L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces
Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).
Nucleic Acids Res. 2002 Jan 1;30(1):69-72.
Le Crom S, Devaux F, Jacq C, Marc P. yMGV: helping biologists with yeast microarray data
mining. Nucleic Acids Res. 2002 Jan; 30: 76-79.
Marc P, Devaux F, Jacq C. yMGV: a database for visualization and data mining of published
genome-wide yeast expression data. Nucleic Acids Res. 2001 Jul 1;29(13):E63-3.
Data Standardization
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Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J,
Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF,
Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J,
Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment
(MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec;29(4):365-71.
Probe design
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Tomiuk S, Hofmann K. Microarray probe selection strategies. Brief Bioinform. 2001
Dec;2(4):329-40.
Data Annotation
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Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for
high-throughput analysis of gene expression. Nat Genet. 2001 May;28(1):21-28.
Promoter analysis and pathway reconstruction
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Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial
analysis of promoter elements. Nat Genet 2001 Oct;29(2):153-9
Wagner A. Estimating coarse gene network structure from large-scale gene perturbation data.
Genome Res. 2002 Feb;12(2):309-15.
Wessels LF, van Someren EP, Reinders MJ. A comparison of genetic network models. Pac
Symp Biocomput. 2001;:508-19.
General microarray information
Microarray:
http://ihome.cuhk.edu.hk/~b400559/array.html
Microarray softwares
http://ihome.cuhk.edu.hk/~b400559/arraysoft.html
Microarray articles:
http://ihome.cuhk.edu.hk/~b400559/journalwatch.html
Microarray books:
http://ihome.cuhk.edu.hk/~b400559/book_mray.html
Other informative microarray portals:
http://www.ii.uib.no/~inge/micro/
Dr. Matern DNA microarrays homepage contains a lot of links to microarray information
http://www.ensam.inra.fr/biochimie/plant_arrays/index.html
Dr. Inge Jonassen homepage contains well categorized key publications on various aspect of
microarray
http://www.ensam.inra.fr/biochimie/plant_arrays/index.html
Plant Arrays information hosted in WWW Virtual Library
http://linkage.rockefeller.edu/wli/microarray/
This site maintained by Dr. WentianLi in Rockefeller University contains a very comprehensive
collection of papers with emphasis on analysis of microarray data.