The Longhorn Array Database (LAD): An open-source, MIAME compliant implementation of the Stanford Microarray database (SMD)

被引：63

作者：

Killion, PJ

Sherlock, G

Iyer, VR ^{[1
]}

机构：

[1] Univ Texas, Inst Mol & Cellular Biol, Sect Mol Genet & Microbiol, Austin, TX 78712 USA

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

来源：

BMC BIOINFORMATICS | 2003年 / 4卷 / 1期

关键词：

Relational Database; Microarray Database; Biological Annotation; Stanford Microarray Database; Open Source Version;

D O I：

10.1186/1471-2105-4-32

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. Description: The Longhorn Array Database ( LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at http:// www.longhornarraydatabase.org Conclusions: Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data.

引用

页数：6

共 11 条

[1]

BALL CA, 2003, DNA MICROARRAYS MOL, P552

[2] 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

[3] ArrayExpress - a public repository for microarray gene expression data at the EBI [J].

Brazma, A ;

Parkinson, H ;

Sarkans, U ;

Shojatalab, M ;

Vilo, J ;

Abeygunawardena, N ;

Holloway, E ;

Kapushesky, M ;

Kemmeren, P ;

Lara, GG ;

Oezcimen, A ;

Rocca-Serra, P ;

Sansone, SA .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :68-71

[4] Data management and analysis for gene expression arrays [J].

Ermolaeva, O ;

Rastogi, M ;

Pruitt, KD ;

Schuler, GD ;

Bittner, ML ;

Chen, YD ;

Simon, R ;

Meltzer, P ;

Trent, JM ;

Boguski, MS .

NATURE GENETICS, 1998, 20 (01) :19-23

[5]

Gardiner-Garden M, 2001, Brief Bioinform, V2, P143, DOI 10.1093/bib/2.2.143

[6] The Stanford Microarray Database: data access and quality assessment tools [J].

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 .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :94-96

[7] Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF [J].

Iyer, VR ;

Horak, CE ;

Scafe, CS ;

Botstein, D ;

Snyder, M ;

Brown, PO .

NATURE, 2001, 409 (6819) :533-538

[8] Characterizing the physical genome [J].

Pollack, JR ;

Iyer, VR .

NATURE GENETICS, 2002, 32 (Suppl 4) :515-521

[9]

Saal LH, 2002, GENOME BIOL, V3

[10] The Stanford Microarray Database [J].

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 .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :152-155

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