The Stanford Microarray Database: implementation of new analysis tools and open source release of software

Demeter, János; Beauheim, Catherine C; Gollub, Jeremy; Hernandez‐Boussard, Tina; Jin, Heng; Maier, Donald; Matese, John C.; Nitzberg, Michael; Wymore, Farrell; Zachariah, Zachariah K.; Brown, Patrick O.; Sherlock, Gavin; Ball, Catherine A.

doi:10.1093/nar/gkl1019

Cited by 149 publications

(121 citation statements)

References 13 publications

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“…First, we extracted microarray data from nine macaques before, and 2 or 3 days post infection from the public access website of the Stanford Microarray Database (SMD). 17 Next, we identified the genes that significantly changed in expression in PB cells of infected macaques by Significance Analysis of Microarrays (SAM). 18 At a false discovery rate of 5%, 911 genes showed a significant change in expression after smallpox infection.…”

Section: Resultsmentioning

confidence: 99%

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Expression of a pathogen-response program in peripheral blood cells defines a subgroup of Rheumatoid Arthritis patients

et al. 2007

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Rheumatoid arthritis (RA) is a heterogeneous disease with unknown etiology. Here we aimed to distinguish RA subtypes based on peripheral blood (PB) gene expression profiles in comparison with a pathogen-response transcriptional program. PB was obtained from 35 RA patients and 15 healthy individuals. For expression profiling we used DNA microarrays. A combined cluster analysis of RA and control samples together with samples from a viral infection model revealed that the gene expression profile of a subgroup of RA patients (RA A ) was reminiscent to that of poxvirus-infected macaques. Statistical analysis, followed by Gene Ontology analysis of the RA A patients confirmed that these patients form a distinct group, with activation of several host defense mechanisms that resemble a common host-pathogen response. Analysis of the promoter region of genes that were overexpressed in the RA A patients, revealed an enrichment of transcription factor binding sites for NFkB and interferon-activated transcription factors. Moreover, this subgroup of RA patients expressed significantly increased titers of anti-cyclic citrullinated peptide antibodies. We conclude that activation of a host-pathogen response defines a subgroup of RA patients characterized by increased autoreactivity against citrullinated proteins.

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Section: Resultsmentioning

confidence: 99%

“…Data were stored and pre-analyzed in the SMD 17 at http://genome-www.stanford.edu/microarray. Data are expressed as log 2 ratios of fluorescence intensities of the experimental and the common reference sample.…”

Section: Data Filtering and Analysismentioning

confidence: 99%

Expression of a pathogen-response program in peripheral blood cells defines a subgroup of Rheumatoid Arthritis patients

et al. 2007

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“…Arrays were scanned with the Agilent microarray scanner, and the data were analyzed with Agilent's "Feature Extraction" software. All raw and normalized microarray data for this paper are available from the Stanford Microarray Database (Demeter et al 2007), where they can be retrieved for further analysis. In addition, they have also been deposited in GEO (Edgar and Barrett 2006), under accession number GSE12177.…”

Section: Array-cgh Protocolmentioning

confidence: 99%

“…To determine the relatedness among strains, microarray data were clustered in SMD (Demeter et al 2007), which uses XCluster, using the Pearson correlation as the metric of similarity.…”

Section: Microarray Data Clusteringmentioning

confidence: 99%

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

Dunn¹,

Sherlock²

2008

Genome Res.

259

391

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Inter-specific hybridization leading to abrupt speciation is a well-known, common mechanism in angiosperm evolution; only recently, however, have similar hybridization and speciation mechanisms been documented to occur frequently among the closely related group of sensu stricto Saccharomyces yeasts. The economically important lager beer yeast Saccharomyces pastorianus is such a hybrid, formed by the union of Saccharomyces cerevisiae and Saccharomyces bayanus-related yeasts; efforts to understand its complex genome, searching for both biological and brewing-related insights, have been underway since its hybrid nature was first discovered. It had been generally thought that a single hybridization event resulted in a unique S. pastorianus species, but it has been recently postulated that there have been two or more hybridization events. Here, we show that there may have been two independent origins of S. pastorianus strains, and that each independent group—defined by characteristic genome rearrangements, copy number variations, ploidy differences, and DNA sequence polymorphisms—is correlated with specific breweries and/or geographic locations. Finally, by reconstructing common ancestral genomes via array-CGH data analysis and by comparing representative DNA sequences of the S. pastorianus strains with those of many different S. cerevisiae isolates, we have determined that the most likely S. cerevisiae ancestral parent for each of the independent S. pastorianus groups was an ale yeast, with different, but closely related ale strains contributing to each group’s parentage.

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“…Statistical differences between patients with and without circulating anti-centromere antibodies (a) were tested by Student's t-test; statistical differences between patients with and without digital ulcers (b) were tested by Mann-Whitney t-test. Data filtering and analysis of microarray data Data were stored and pre-analyzed in the Stanford Microarray Database (SMD) 29 at http://genomewww.stanford.edu/microarray. Data are expressed as log2 ratios of fluorescence intensities of the experimental and reference samples.…”

Section: Sample Preparation For Array Hybridizationmentioning

confidence: 99%

Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers

et al. 2009

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The Stanford Microarray Database: implementation of new analysis tools and open source release of software

Cited by 149 publications

References 13 publications

Expression of a pathogen-response program in peripheral blood cells defines a subgroup of Rheumatoid Arthritis patients

Expression of a pathogen-response program in peripheral blood cells defines a subgroup of Rheumatoid Arthritis patients

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers

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