The Stanford Microarray Database: data access and quality assessment tools

By J. Gollub, Catherine A. Ball, G. Binkley, J. Demeter, D. Finkelstein, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, Miroslava Kaloper, J. Matese and 4 more. Nucleic Acids Res., 2003

363 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cab45509a226298d753b48eec24927cb65afa2d4

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Citations in the corpus

Defining transcription modules using large-scale gene expression data (2004, background): “The availability of this highthroughput technology has led to the accumulation of large datasets comprising thousands of expression profiles for a variety of organisms ranging from bacteria to human (Gollub et al., 2003).”
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks (2005, methodology): “We define the probability of a true interaction as a logistic function of three observed random variables on a pair of proteins: (1) the number of times an interaction between the proteins was experimentally observed; (2) the Pearson correlation coefficient of expression measurements for the corresp”
GC–MS libraries for the rapid identification of metabolites in complex biological samples (2005, background): “over 3500 DNA-microarrays of 12 distinct organisms, including bacteria, plants and animals, was the first implementation to fulfil this aim [3].”
Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast (2004, methodology): “Log 2 median ratios were retrieved from SMD and exported into Microsoft (Redmond, Washington, United States) Excel after filtering for regression correlation of greater than 0.6 (filters for large variations in the ratios of pixels within each spot), CH1I/CH1B of greater than 1.8 (signal over backgr”
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service (2004, methodology): “The spot history is a tool that is available in other microarray databases (8).”
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans (2008, methodology): “In July 2005, we downloaded expression data from the Stanford Microarray Databas”
The Proteomics Protocols Handbook (2005, background): “Short-chain phospholipids have been used to isolate functional membrane protein complexes; however, these molecules interact primarily with the membrane lipids, and there is little if any interaction with the integral membrane proteins (67).”
Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. (2004, background): “¡7/del(7q) Normal karyotype +8 sole Complex karyotype t(8;21)”
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment (2004, neutral): “[20].”
GEMS: A system for automated cancer diagnosis and biomarker discovery from microarray gene expression data (2005, methodology): “We identified 193 primary gene expression-based cancer diagnosis studies using the ONCOMINE Cancer Microarray Database [8], the UPITT Cancer Gene Expression Data Set Link Database [9], and the Stanford Microarray Database [10].”
GMD@CSB.DB: the Golm Metabolome Database (2005, methodology): “The widely shared experimental approach facilitated the establishment of expression profile related databases, such as the Stanford Microarray Database [SMD (Gollub et al., 2003)], TAIR or NCBI–GEO (Edgar et al.”
A novel method for accurate operon predictions in all sequenced prokaryotes (2005, methodology): “edu/microarray, [28]), for Synechocystis from the Kyoto Encyclopedia of Genes and Genomes (49 arrays from http:// www.”
The xenobiotic β‐aminobutyric acid enhances Arabidopsis thermotolerance (2008, methodology): “edu//) under experiment IDs 33704, 33705, 33706 and 33707 (BABA 1–4) (Gollub et al., 2003).”