Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 The Stanford Microarray Database: data access and quality assessment tools.

Literature DB >> 12519956

The Stanford Microarray Database: data access and quality assessment tools.

Jeremy Gollub¹, Catherine A Ball, Gail Binkley, Janos Demeter, David B Finkelstein, Joan M Hebert, Tina Hernandez-Boussard, Heng Jin, Miroslava Kaloper, John C Matese, Mark Schroeder, Patrick O Brown, David Botstein, Gavin Sherlock.

Abstract

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.

Mesh：

Year: 2003 PMID： 12519956 PMCID： PMC165525 DOI： 10.1093/nar/gkg078

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

10 in total

1. Genome-wide location and function of DNA binding proteins.

Authors: B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal: Science Date: 2000-12-22 Impact factor: 47.728

2. Genome-wide analysis of DNA copy-number changes using cDNA microarrays.

Authors: J R Pollack; C M Perou; A A Alizadeh; M B Eisen; A Pergamenschikov; C F Williams; S S Jeffrey; D Botstein; P O Brown
Journal: Nat Genet Date: 1999-09 Impact factor: 38.330

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

Authors: A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal: Nat Genet Date: 2001-12 Impact factor: 38.330

4. Profiling protein function with small molecule microarrays.

Authors: Nicolas Winssinger; Scott Ficarro; Peter G Schultz; Jennifer L Harris
Journal: Proc Natl Acad Sci U S A Date: 2002-08-07 Impact factor: 11.205

5. Large-scale temporal gene expression mapping of central nervous system development.

Authors: X Wen; S Fuhrman; G S Michaels; D B Carr; S Smith; J L Barker; R Somogyi
Journal: Proc Natl Acad Sci U S A Date: 1998-01-06 Impact factor: 11.205

6. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

Authors: M Schena; D Shalon; R W Davis; P O Brown
Journal: Science Date: 1995-10-20 Impact factor: 47.728

7. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.

Authors: C M Perou; S S Jeffrey; M van de Rijn; C A Rees; M B Eisen; D T Ross; A Pergamenschikov; C F Williams; S X Zhu; J C Lee; D Lashkari; D Shalon; P O Brown; D Botstein
Journal: Proc Natl Acad Sci U S A Date: 1999-08-03 Impact factor: 11.205

8. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

Authors: T R Golub; D K Slonim; P Tamayo; C Huard; M Gaasenbeek; J P Mesirov; H Coller; M L Loh; J R Downing; M A Caligiuri; C D Bloomfield; E S Lander
Journal: Science Date: 1999-10-15 Impact factor: 47.728

9. Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.

Authors: F Forozan; E H Mahlamäki; O Monni; Y Chen; R Veldman; Y Jiang; G C Gooden; S P Ethier; A Kallioniemi; O P Kallioniemi
Journal: Cancer Res Date: 2000-08-15 Impact factor: 12.701

10. Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors: Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal: Genome Biol Date: 2002-08-23 Impact factor: 13.583

10 in total

103 in total

10. MgrA, an orthologue of Mga, Acts as a transcriptional repressor of the genes within the rlrA pathogenicity islet in Streptococcus pneumoniae.

Authors: Carolyn Hemsley; Elizabeth Joyce; David L Hava; Amita Kawale; Andrew Camilli
Journal: J Bacteriol Date: 2003-11 Impact factor: 3.490

The Stanford Microarray Database: data access and quality assessment tools.

1. Genome-wide location and function of DNA binding proteins.

2. Genome-wide analysis of DNA copy-number changes using cDNA microarrays.

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

4. Profiling protein function with small molecule microarrays.

5. Large-scale temporal gene expression mapping of central nervous system development.

6. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

7. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.

8. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

9. Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.

10. Design and implementation of microarray gene expression markup language (MAGE-ML).

1. Gene expression in the normal adult human kidney assessed by complementary DNA microarray.

2. Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin.

3. PlantGDB, plant genome database and analysis tools.

4. ArrayProspector: a web resource of functional associations inferred from microarray expression data.

5. CARRIE web service: automated transcriptional regulatory network inference and interactive analysis.

6. Consequences of a deletion in dspA on transcript accumulation in Synechocystis sp. strain PCC6803.

7. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.

8. Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.

9. A complex-based reconstruction of the Saccharomyces cerevisiae interactome.

10. MgrA, an orthologue of Mga, Acts as a transcriptional repressor of the genes within the rlrA pathogenicity islet in Streptococcus pneumoniae.