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: ,

URL: or

Image analysis

  1. 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.
  2. Yang YH, Buckley MJ, Speed TP. Analysis of cDNA microarray images.Brief Bioinform. 2001 Dec;2(4):341-9.
  3. 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

  1. Sherlock G. Analysis of large-scale gene expression data. Brief Bioinform. 2001 Dec;2(4):350-62.
  2. Wu TD. Analysing gene expression data from DNA microarrays to identify candidate genes. J Pathol. 2001 Sep;195(1):53-65.
  3. Quackenbush J. Computational genetics computational analysis of microarray data. Nat Rev Genet. 2001 Jun;2(6):418-27.
  4. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Basic microarray analysis: grouping and feature reduction. Trends Biotechnol. 2001. May; 19:189-193
  5. 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

  1. 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

  1. Gardiner-Garden M, Littlejohn TG. A comparison of microarray databases. Brief Bioinform. 2001 May;2(2):143-58.

Public Database

  1. Miles MF. OPINION Microarrays: lost in a storm of data? Nat Rev Neurosci. 2001 Jun;2(6):441-3.
  2. Becker KG. OPINION The sharing of cDNA microarray data. Nat Rev Neurosci. 2001 Jun;2(6):438-40.
  3. Geschwind DH. OPINION Sharing gene expression data: an array of options. Nat Rev Neurosci. 2001 Jun;2(6):435-8.
  4. 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

  1. 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

  1. Bono H, Kasukawa T, Hayashizaki Y, Okazaki Y. READ: RIKEN Expression Array Database. Nucleic Acids Res. 2002 Jan; 30: 211-213.

SMD

  1. 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.

SGD

  1. 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.

yMGV

  1. 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.
  2. 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

  1. 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

  1. Tomiuk S, Hofmann K. Microarray probe selection strategies. Brief Bioinform. 2001 Dec;2(4):329-40.

Data Annotation

  1. 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

  1. Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 2001 Oct;29(2):153-9
  2. Wagner A. Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res. 2002 Feb;12(2):309-15.
  3. Wessels LF, van Someren EP, Reinders MJ. A comparison of genetic network models. Pac Symp Biocomput. 2001;:508-19.

General microarray information

Microarray:

Microarray softwares

Microarray articles:

Microarray books:

Other informative microarray portals:

Dr. Matern DNA microarrays homepage contains a lot of links to microarray information

Dr. Inge Jonassen homepage contains well categorized key publications on various aspect of microarray

Plant Arrays information hosted in WWW Virtual Library

This site maintained by Dr. WentianLi in Rockefeller University contains a very comprehensive collection of papers with emphasis on analysis of microarray data.