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SMD specifications

Information


Unique identifier OMICS_00870
Name SMD
Alternative name Stanford Microarray Database
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Catherine A. Ball

Publications for Stanford Microarray Database

SMD citations

 (62)
library_books

A feature selection method based on multiple kernel learning with expression profiles of different types

2017
BioData Min
PMCID: 5288949
PMID: 28184251
DOI: 10.1186/s13040-017-0124-x

[…] tained by measuring the expressions of genes or miRNAs simultaneously. Researchers can acquire these different expression data from several public databases, such as Gene Expression Omnibus (GEO) [], Stanford Microarray Database (SMD) [], ArrayExpress [] and The Cancer Genome Atlas (TCGA) []. TCGA is the largest cancer genome sequencing project, which plan to sequence and organize 10,000 cancer ge […]

library_books

Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

2016
Sci Rep
PMCID: 5157009
PMID: 27976738
DOI: 10.1038/srep39237

[…] O in previous studies, namely 1) correlation network of genetic interactions from DRYGIN (http://drygin.ccbr.utoronto.ca/DOWNLOAD/sgadata_costanzo2010_correlations.txt.gz), co-expression network from Stanford Microarray Database (SMD)(Provided by Michael Kramer), probabilistic functional gene network from YeastNet (v3)(http://www.inetbio.org/yeastnet/download.php?type=1), and network of physical i […]

library_books

Recent Advances in Understanding the Molecular Mechanisms Regulating the Root System Response to Phosphate Deficiency in Arabidopsis

2016
Curr Genomics
PMCID: 4955032
PMID: 27499680
DOI: 10.2174/1389202917666160331201812

[…] ponse.Fortuitously, multiple sets of Arabidopsis microarray data have been assembled in various available databases, as well as data mining and analysis tool boxes such as TAIR [], NASCArrays [], the Stanford Microarray Database [] and GENEVESTIGATOR []. These data sources can be combined with several meta-analysis tools using a guilt-by-association principle to help visualise correlated gene expr […]

library_books

MIEN1, a novel interactor of Annexin A2, promotes tumor cell migration by enhancing AnxA2 cell surface expression

2015
Mol Cancer
PMCID: 4536591
PMID: 26272794
DOI: 10.1186/s12943-015-0428-8

[…] d to assess MIEN1 expression in breast cancer molecular subtypes. Bc-GenEXMiner analyzes available gene expression data sets from repositories such as Gene Expression Omnibus (GEO), Array Express and Stanford microarray database [–]. The analysis was performed through a built-in robust single sample predictor (SSP) classification (RSSPC), which includes intersection of three SSPs []. The UCSC Canc […]

library_books

limma powers differential expression analyses for RNA sequencing and microarray studies

2015
Nucleic Acids Res
PMCID: 4402510
PMID: 25605792
DOI: 10.1093/nar/gkv007

[…] ly supports formats written by many different image analysis programs including GenePix, Agilent Feature Extraction, ArrayVision, BlueFuse, ImaGene, QuantArray and SPOT (Table ). It also supports the Stanford Microarray Database format. Output in other formats can be read if the appropriate column names are supplied. Two-colour and single-channel data are both supported. Illumina BeadChips need sp […]

library_books

The OncoFinder algorithm for minimizing the errors introduced by the high throughput methods of transcriptome analysis

2014
Front Mol Biosci
PMCID: 4428387
PMID: 25988149
DOI: 10.3389/fmolb.2014.00008

[…] et al., ).This information has resulted in the accumulation of the large collections of public gene expression datasets including the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/), Stanford Microarray Database (http://smd.stanford.edu/), Cancer Genome Atlas (https://tcga-data.nci.nih.gov/), EBI ArrayExpress (http://www.ebi.ac.uk/arrayexpress/), mAdb (https://madb.nci.nih.gov/), […]

Citations

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SMD institution(s)
Department of Genetics, Center for Clinical Sciences Research, Stanford University, Stanford, CA, USA

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