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Transcription profiling of peripheral blood leukocyte genomic response one day post traumatic injury may predict early respiratory recovery

ABSTRACT: This data was used as an example to illustrate a computational method for assessing statistical significance in microarray experiments Contributed by 'The Inflammation and the Host Response to Injury Collaborative Research Program.' Keywords: Two group comparison Genomic response one day post traumatic injury was compared between patients having early or late respiratory recovery

ORGANISM(S): Homo sapiens

SUBMITTER: IDDC Inflammation & the Host Response to Injury

PROVIDER: E-GEOD-13488 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Assessing statistical significance in microarray experiments using the distance between microarrays.

Hayden Douglas D Lazar Peter P Schoenfeld David D

PloS one 20090616 6

We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations. For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis. The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data. An R software package, permtest, implementing the method is freely available ...[more]

PMID: 19529777

Similar Datasets

Peripheral blood leukocyte genomic response one day post traumatic injury may predict early respiratory recovery

Project description:This data was used as an example to illustrate a computational method for assessing statistical significance in microarray experiments Contributed by 'The Inflammation and the Host Response to Injury Collaborative Research Program.' Keywords: Two group comparison

2011-12-01 | GSE13488 | GEO

Astrocyte-specific deletion of SOX2 promotes recovery after traumatic brain injury

Project description:Injury to the adult brain induces activation of resident astrocytes, which serves as a compensatory response modulating tissue damage and recovery. However, the mechanism governing astrocyte activation and the role of reactive astrocytes remain largely unknown. Here we show that SOX2, a transcription factor critical for stem cells and brain development, is also required for injury-induced activation of adult cortical astrocytes. Genome-wide ChIP-seq analysis reveals that SOX2 binds to regulatory regions of genes associated with signaling pathways controlling reactive gliosis, such as Socs3, Nr2e1, Notch1, and Akt2. Inducible deletion of Sox2 in adult astrocytes greatly diminishes their response to traumatic injury and, most unexpectedly, restricts injury-induced cortical loss. Together, these results uncover an essential role of SOX2 in terminally differentiated cells and implicate that SOX2-dependent reactive astrocytes may be targeted for regeneration after traumatic brain injury.

2018-02-22 | GSE85213 | GEO

Gene response to major burn injuries

Project description:Blood was sampled from severe burns patients over time as well as healthy subjects. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™. The Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program Blood was sampled from 244 severe burns patients over time as well as 35 healthy subjects who consented to blood sampling. Study subjects were treated under standard operating procedures to minimize treatment variations. Patients had burns covering >20% of the total body surface area and were admitted within 96 hours of injury. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™.

2013-02-12 | E-GEOD-37069 | biostudies-arrayexpress

Gene expression profiles after traumatic brain injury

Project description:Time dependent-profiles in the gene expression level following lateral moderate fluid percussion injury in the rat brain We used microarray to elucidate relationship between the alteration of gene expression levels and the progression of brain damages following traumatic brain injury. To examine the levels of gene expression in the early phase of traumatic brain injury, we analyzed the gene expression at 3, 6, 12, and 48 h after trauma using the lateral moderate fluid percussion TBI model. The ratios of the gene expression level were compared between chips corresponding to the 3, 6 and 12 h fluid percussion groups and the sham group chips. On the other hand, the rations of gene expression level after 48 h FPI were compared with 48 h sham chip, because the gene expression levels of 48 h sham chip were distinct from sham group chips (3, 6 and 12 h) in the cluster and principal components analyses.

2010-12-07 | E-GEOD-24047 | biostudies-arrayexpress

Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury

Project description:Background: Traumatic brain injury is a medical event of global concern, and a growing body of research suggests that circular RNA can play very important roles in traumatic brain injury. To explore the functions of more novel and valuable circular RNA in traumatic brain injury response, a moderate traumatic brain injury in rat was established and a comprehensive analysis of circular RNA expression profiles in rat cerebral cortex was done. Results: As a result, 301 up-regulated and 284 down-regulated circular RNAs were obtained in moderate traumatic brain injury rats, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed based on the circular RNA’s host genes, and a circRNA-miRNA interaction network based on differentially expressed circular RNAs was constructed. Also, four circular RNAs were validated by RT-qPCR and sanger sequencing. Conclusion: This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.

2022-01-15 | GSE193521 | GEO

The dentate gyrus after traumatic brain injury [miRNA]

Project description:Analysis of the dentate gyrus of traumatic brain injury model. Results provide insight into the molecular mechanism underlying TBI.

2017-02-25 | GSE86614 | GEO

The dentate gyrus after traumatic brain injury [mRNA]

Project description:Analysis of the dentate gyrus of traumatic brain injury model. Results provide insight into the molecular mechanism underlying TBI.

2017-02-25 | GSE86579 | GEO

Exercise intensity and sex alter neurometabolic, transcriptional, and functional recovery following traumatic brain injury.

Project description:In order to assess the impact of treadmill exercise on traumatic brain injury outcomes, we subjected male and female swiss webster mice to a controlled cortical impact (CCI), followed by 10 days of sedentary, low-, moderate-, or high-intensity treadmill exercise. Outcome measures included neurometabolic function, cognitive recovery, oxidative stress, pathophysiology, and single nuclei RNA sequencing (snRNA seq). The snRNA seq study was conducted on both male and female mice, and included a total of 2 replicates (each was a pool of 2 tissue samples) from each of the following groups: male sham sedentary, male CCI sedentary, male CCI low, male CCI high, female sham sedentary, female CCI sedentary, female CCI low, female CCI high. Our data reveal exercise intensity- and sex-dependent effects of treadmill exercise following injury. Transcriptomic changes were largely limited to the low-intensity exercised CCI males.

2023-08-01 | GSE226072 | GEO

Gene expression profiles after traumatic brain injury

2010-12-07 | GSE24047 | GEO

Metabolomic Profiles of Recovery from Traumatic Brain Injury

Project description:We hypothesize that differences between the metabolome of TBI patients achieving full recovery at 3 months post-injury and those with protracted recovery will provide insights into the biology of recovery and yield novel biomarkers for predicting protracted recovery. To test our hypothesis, we will perform a case-control study examining the metabolomic profile of 128 TBI patients, 18 years and older, who either have complete functional recovery at 3 months post-injury or have functional decline at 3 months post-injury. Subjects were selected from an ongoing prospective cohort of traumatic brain injury (Head Injury Serum Markers for Assessing Response to Trauma, HeadSMART. Funding for HeadSMART was provided by ImmunArray.

2017-06-19 | ST000721 | MetabolomicsWorkbench

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