The Stanford Microarray Database: data access and quality assessment tools

被引：240

作者：

Gollub, J

Ball, CA

Binkley, G

Demeter, J

Finkelstein, DB

Hebert, JM

Hernandez-Boussard, T

Jin, H

Kaloper, M

Matese, JC

Schroeder, M

Brown, PO

Botstein, D

Sherlock, G

机构：

[1] Stanford Univ, Dept Genet, Ctr Clin Sci Res, Stanford, CA 94305 USA

[2] Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA

[3] Affymetrix Inc, Emeryville, CA 94608 USA

[4] Stanford Univ, Ctr Clin Sci Res, Stanford Funct Genom Facil, Stanford, CA 94305 USA

[5] Stanford Univ, Sch Med, Dept Biochem, Howard Hughes Med Inst, Stanford, CA 94305 USA

来源：

NUCLEIC ACIDS RESEARCH | 2003年 / 31卷 / 01期

关键词：

D O I：

10.1093/nar/gkg078

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3500 microarrays, including data from 85 publications, and this total is increasing rapidly. In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis.

引用

页码：94 / 96

页数：3

共 13 条

[1]

[Anonymous], 2002, Nature, V419, P323

[2] A guide to microarray experiments - an open letter to the scientific journals [J].

Ball, CA ;

Sherlock, G ;

Parkinson, H ;

Rocca-Sera, P ;

Brooksbank, C ;

Causton, HC ;

Cavalieri, D ;

Gaasterland, T ;

Hingamp, P ;

Holstege, F ;

Ringwald, M ;

Spellman, P ;

Stoeckert, CJ ;

Stewart, JE ;

Taylor, R ;

Brazma, A ;

Quackenbush, J .

LANCET, 2002, 360 (9338) :1019-1019

[3] Minimum information about a microarray experiment (MIAME) - toward standards for microarray data [J].

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, FCP ;

Kim, IF ;

Markowitz, V ;

Matese, JC ;

Parkinson, H ;

Robinson, A ;

Sarkans, U ;

Schulze-Kremer, S ;

Stewart, J ;

Taylor, R ;

Vilo, J ;

Vingron, M .

NATURE GENETICS, 2001, 29 (04) :365-371

[4]

Forozan F, 2000, CANCER RES, V60, P4519

[5] Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring [J].

Golub, TR ;

Slonim, DK ;

Tamayo, P ;

Huard, C ;

Gaasenbeek, M ;

Mesirov, JP ;

Coller, H ;

Loh, ML ;

Downing, JR ;

Caligiuri, MA ;

Bloomfield, CD ;

Lander, ES .

SCIENCE, 1999, 286 (5439) :531-537

[6] Distinctive gene expression patterns in human mammary epithelial cells and breast cancers [J].

Perou, CM ;

Jeffrey, SS ;

Van de Rijn, M ;

Rees, CA ;

Eisen, MB ;

Ross, DT ;

Pergamenschikov, A ;

Williams, CF ;

Zhu, SX ;

Lee, JCF ;

Lashkari, D ;

Shalon, D ;

Brown, PO ;

Botstein, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (16) :9212-9217

[7] Genome-wide analysis of DNA copy-number changes using cDNA microarrays [J].

Pollack, JR ;

Perou, CM ;

Alizadeh, AA ;

Eisen, MB ;

Pergamenschikov, A ;

Williams, CF ;

Jeffrey, SS ;

Botstein, D ;

Brown, PO .

NATURE GENETICS, 1999, 23 (01) :41-46

[8] Genome-wide location and function of DNA binding proteins [J].

Ren, B ;

Robert, F ;

Wyrick, JJ ;

Aparicio, O ;

Jennings, EG ;

Simon, I ;

Zeitlinger, J ;

Schreiber, J ;

Hannett, N ;

Kanin, E ;

Volkert, TL ;

Wilson, CJ ;

Bell, SP ;

Young, RA .

SCIENCE, 2000, 290 (5500) :2306-+

[9] QUANTITATIVE MONITORING OF GENE-EXPRESSION PATTERNS WITH A COMPLEMENTARY-DNA MICROARRAY [J].

SCHENA, M ;

SHALON, D ;

DAVIS, RW ;

BROWN, PO .

SCIENCE, 1995, 270 (5235) :467-470

[10]

Spellman PT, 2002, GENOME BIOL, V3

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