Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Viral Microarray - Control Set

ABSTRACT: Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.

ORGANISM(S): West Nile virus

SUBMITTER: Omar Jabado

PROVIDER: E-GEOD-21317 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Nonparametric methods for the analysis of single-color pathogen microarrays.

Jabado Omar J OJ Conlan Sean S Quan Phenix-Lan PL Hui Jeffrey J Palacios Gustavo G Hornig Mady M Briese Thomas T Lipkin W Ian WI

BMC bioinformatics 20100628

<h4>Background</h4>The analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied.<h4>Results</h4>Positive predictive value and f ...[more]

PMID: 20584331

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Project description:Organisms cope with physiological stressors through acclimatizing mechanisms in the short-term, and through adaptive mechanisms over evolutionary timescales. Whereas the former offer a consistent and largely predictable buffer against stressors, myriad paths of adaptation are often possible. Our work examined whether knowledge of acclimatizing responses could be informative ofM-BM- aspects of future adaptation, using as a model system a strain of Methylobacterium extorquens AM1 that was experimentally engineered and then evolved with a novel central metabolism. The engineered strain is markedly slower and less fit than wild-type, which is reflected in microarray analyses by hundreds of genes with differential expression, and also altered levels NAD(P)(H) metabolites. Yet after 600 generations of evolution in the lab, eight replicate populations founded from an engineered ancestor showed substantial but variable improvements in growth using the engineered metabolic pathway. Using information from wild-type, engineered, and adapted physiological states, we determined the extent to which physiological processes were restored, unrestored, reinforced, or novel after experimental evolution. Overall, we found that the vast majority of gene expression perturbations from the engineered strain are restored to wild-type like conditions after experimental evolution but were accompanied by a modest number of unrestored processes, varying instances of novel expression, and a few rare instances where expression changes from acclimation were reinforced through adaptive evolution. One such example was in the reinforced up-regulation of pntAB transhydrogenase, whose increased expression and activity correlated with the restoration of NAD(P)(H) metabolism towards wild-type levels and with increased growth rate in the evolved lineages. Thus, while trajectories of physiological adaptation may still be difficult to predict a priori, our results demonstrate that information from acclimatizing responses can provide a M-bM-^@M-^\directionM-bM-^@M-^] to hypothesize which changes in physiology arose as a consequence of adaptation versus those that may have caused itM-BM- . Single-color microarray hydridization of total RNA isolated from mid-exponentially grown cultures of wildtype, engineered, and eight experimentally evolved populations of Methylobacterium extorquens AM1, each represented by three biological replicates

Dataset Information

Viral Microarray - Control Set

Publications

Nonparametric methods for the analysis of single-color pathogen microarrays.

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