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239
Limma: linear models for microarray data
- Bioinformatics and Computational Biology Solutions using R and Bioconductor
, 2005
"... This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.Contents ..."
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Cited by 774 (13 self)
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This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.Contents
limma powers differential expression analyses for RNA-sequencing and microarray studies
- Nucleic Acids Res
, 2015
"... RNA-sequencing and microarray studies (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. ..."
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Cited by 32 (4 self)
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RNA-sequencing and microarray studies (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters.
Interferome v2.0: an updated database of annotated interferon-regulated genes. Nucleic Acids Res 41: D1040–1046
, 2013
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An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
- Nucleic Acids Res
, 2009
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doi:10.1093/nar/gkl435 Non-linear analysis of GeneChip arrays
, 2006
"... The application of microarray hybridization theory to Affymetrix GeneChip data has been a recent focus for data analysts. It has been shown that the hyperbolic Langmuir isotherm captures the shape of the signal response to concentration of Affymetrix GeneChips. We demonstrate that existing linear fi ..."
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The application of microarray hybridization theory to Affymetrix GeneChip data has been a recent focus for data analysts. It has been shown that the hyperbolic Langmuir isotherm captures the shape of the signal response to concentration of Affymetrix GeneChips. We demonstrate that existing linear fit methods for extracting gene expression measures are not well adapted for the effect of saturation resulting from surface adsorption processes. In contrast to the most popular methods, we fit background and concentration parameters within a single global fitting routine instead of estimating the background before obtaining gene expression measures. We describe a non-linear multi-chip model of the perfect match signal that effectively allows for the separation of specific and non-specific components of the microarray signal and avoids saturation bias in the high-intensity range. Multimodel inference, incorporated within the fitting routine, allows a quantitative selection of the model that best describes the observed data. The performance of this method is evaluated on publicly available datasets, and comparisons to popular algorithms are presented.
Function of the cytochrome bc1-aa3 branch of the respiratory network in mycobacteria and network adaptation occurring in response to its disruption
- J. Bacteriol. 2005
"... Supplemental material This article cites 39 articles, 15 of which can be accessed free at: ..."
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Cited by 6 (0 self)
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Supplemental material This article cites 39 articles, 15 of which can be accessed free at:
Selection and validation of normalization methods for c-DNA microarrays using within-array replications
, 2007
"... Motivation:Normalizationofmicroarraydataisessentialformultiplearray analyses. Several normalization protocols have been proposed basedondifferentbiologicalorstatisticalassumptions.Afundamental problem arises whether they have effectively normalized arrays. In addition, for agiven array, the question ..."
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Cited by 5 (0 self)
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Motivation:Normalizationofmicroarraydataisessentialformultiplearray analyses. Several normalization protocols have been proposed basedondifferentbiologicalorstatisticalassumptions.Afundamental problem arises whether they have effectively normalized arrays. In addition, for agiven array, the question arises how to choose a methodtomosteffectivelynormalizethemicroarraydata. Results: We propose several techniques to compare the effectiveness of different normalization methods. We approach the problem by constructing statistics to test whether there are any systematic biases in the expression profiles among duplicated spots within an array. The test statistics involve estimating the genewise variances. This is accomplished by using several novel methods, including empirical Bayes methods for moderating the genewise variances and the smoothing methods for aggregating variance information. P-values are estimated based on a normal or chisquare approximation. With estimated P-values, we can choose a most appropriate method to normalize aspecific array and assess the extent to which the systematic biases due to the variations of experimental conditions have been removed. The effectiveness and validity of the proposed methods are convincingly illustrated by a carefully designed simulation study. The method is further illustrated by an application to human placenta cDNAs comprising alarge number of clones with replications, acustomized microarray experiment carrying just afew hundred genes on the study of the molecular roles of Interferons on tumor, and the Agilent microarrays carryingtensofthousandsoftotalRNAsamplesintheMAQCproject on thestudyofreproducibility,sensitivityandspecificityofthe data.
Ecf, an Alternative Sigma Factor from Neisseria gonorrhoeae, Controls Expression of msrAB, Which Encodes Methionine Sulfoxide Reductase
, 2005
"... A DNA microarray was used to identify genes transcribed in Neisseria gonorrhoeae using Ecf, an alternative sigma factor. No differences between the transcriptional profiles of strain FA1090 and a mutant where ecf had been inactivated could be detected when both were grown in vitro. We therefore cons ..."
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Cited by 5 (1 self)
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A DNA microarray was used to identify genes transcribed in Neisseria gonorrhoeae using Ecf, an alternative sigma factor. No differences between the transcriptional profiles of strain FA1090 and a mutant where ecf had been inactivated could be detected when both were grown in vitro. We therefore constructed a gonococcal strain in which Ecf can be overexpressed. Some differentially expressed genes are clustered with ecf on the genome and appear to form a single transcriptional unit. Expression of the gene encoding MsrAB, which possesses methionine sulfoxide reductase activity, was also dependent on Ecf, suggesting that the regulon responds to oxidative damage. Western blotting confirmed that the increased level of MsrAB protein is dependent on the presence of Ecf. Bacterial sigma factors are essential components of the RNA polymerase holoenzyme and determine promoter selectivity and specificity. Bacteria usually contain at least one essential sigma factor, sigma-70, which is necessary for cell viability, as well as a number of accessory sigma factors that are often involved in responses to environmental stimuli or the phase of growth. The relative amount of RNA polymerase holoenzyme containing each sigma factor determines the amplitude
BioMed Central
, 2006
"... Research article Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival ..."
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Research article Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival
Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fedbatch cultivations. Appl Environ Microbiol 74: 7002–7015
, 2008
"... This article cites 69 articles, 23 of which can be accessed free ..."
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Cited by 4 (0 self)
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This article cites 69 articles, 23 of which can be accessed free