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Article
Open AccessPulmonDB: a curated lung disease gene expression database
Chronic Obstructive Pulmonary Disease (COPD) and Idiopathic Pulmonary Fibrosis (IPF) have contrasting clinical and pathological characteristics and interesting whole-genome transcriptomic profiles. However, da...
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Article
Open AccessFirst step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Exploring cellular responses to stimuli using extensive gene expression profiles has become a routine procedure performed on a daily basis. Raw and processed data from these studies are available on public dat...
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Protocol
Comparative Analysis of Gene Expression: Uncovering Expression Conservation and Divergence Between Salmonella enterica Serovar Typhimurium Strains LT2 and 14028S
Different strains of the same organism can share a large amount of their genetic material, the so called core pangenome. Nevertheless, these species can display different lifestyles and it is still not well kn...
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Protocol
Directed Module Detection in a Large-Scale Expression Compendium
Public online microarray databases contain tremendous amounts of expression data. Mining these data sources can provide a wealth of information on the underlying transcriptional networks. In this chapter, we i...
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Article
Transcriptome Analysis of the Rhizosphere Bacterium Azospirillum brasilense Reveals an Extensive Auxin Response
The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate dec...
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Article
Open AccessStress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli
The alarmone (p)ppGpp mediates a global reprogramming of gene expression upon nutrient limitation and other stresses to cope with these unfavorable conditions. Synthesis of (p)ppGpp is, in most bacteria, contr...
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Article
Open AccessQuery-based biclustering of gene expression data using Probabilistic Relational Models
With the availability of large scale expression compendia it is now possible to view own findings in the light of what is already available and retrieve genes with an expression profile similar to a set of gen...
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Article
Open AccessThe Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina
Previous studies in Ascomycetes have shown that the function of gene families of which the size is considerably larger in extant pathogens than in non-pathogens could be related to pathogenicity traits. Howeve...
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Article
The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium
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Article
Open AccessGenome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array
Non-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In the past few years, a growing number of re...
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Article
Open AccessDISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase regulator s...
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Article
Open AccessExpression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation
In a previously published pilot study we explored the performance of microarrays in predicting clinical behaviour of ovarian tumours. For this purpose we performed microarray analysis on 20 patients and estima...
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Article
Open AccessEvaluation of time profile reconstruction from complex two-color microarray designs
As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (...
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Article
Open AccessJoint map** of genes and conditions via multidimensional unfolding analysis
Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expressio...
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Article
Open AccessInferring transcriptional modules from ChIP-chip, motif and microarray data
'ReMoDiscovery' is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data source...
