Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Longitudinal Intra- and Inter-individual variation in T-cell subsets of HIV-infected and uninfected men participating in the LA Multi-Center AIDS Cohort Study.

ABSTRACT: To assess the intra-individual and inter-individuals biological variation and the effect of aging on lymphocyte T-cells subsets.We assessed lymphocyte phenotypes (CD3, CD4, and CD8 T-cells) in 89 HIV-1-infected and 88 uninfected white non-Hispanic men every 6 months, to examine the biological variation for those measurements, and the average change in lymphocyte phenotype over 34 years.The markers showed significant intra-individuality in HIV-infected and uninfected individuals with index of individuality of <1.4. No mean changes were seen over the 34 years, with the exception of percentage CD4T-cells in HIV-uninfected individuals.In the pre-HAART era, HIV-infected individuals experienced an increase in mean absolute CD3 T-cell numbers (11.21?cells/?L, P = 0.02) and absolute CD8 T-cell numbers (34.57?cell/?l, P?

SUBMITTER: Aziz N

PROVIDER: S-EPMC6799419 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Longitudinal Intra- and Inter-individual variation in T-cell subsets of HIV-infected and uninfected men participating in the LA Multi-Center AIDS Cohort Study.

Aziz Najib N Jamieson Beth D BD Quint Joshua J JJ Martinez-Maza Otoniel O Chow Marianne M Detels Roger R

Medicine 20191001 41

To assess the intra-individual and inter-individuals biological variation and the effect of aging on lymphocyte T-cells subsets.We assessed lymphocyte phenotypes (CD3, CD4, and CD8 T-cells) in 89 HIV-1-infected and 88 uninfected white non-Hispanic men every 6 months, to examine the biological variation for those measurements, and the average change in lymphocyte phenotype over 34 years.The markers showed significant intra-individuality in HIV-infected and uninfected individuals with index of ind ...[more]

PMID: 31593126

Similar Datasets

Intra- and inter-individual genetic differences in gene expression

2009-12-31 | GSE8358 | GEO

Intra- and inter-individual genetic differences in gene expression

Project description:Each expressed gene was tested for differential expression in three mouse tissues (Brain, Kidney, Liver) in a direct comparison of SJL/J vs. C57BL/6J Keywords: direct comparison, multiple tissues Whole RNA from a pool of 5 SJL/J mice was compared to a pool of RNA from C57BL/6J mice with three technical replicates per tissue, no dye swaps.

2010-05-16 | E-GEOD-8358 | biostudies-arrayexpress

Intra-individual and inter-individual variability in daily sitting time and MVPA.

Project description:Little is known about how much variability exists in free-living sitting time within individuals. The purpose of this study was to examine intra-individual variability of objectively determined daily sitting time and to determine if this variability was related to weekly averages of sitting duration or recommended moderate-vigorous physical activity (MVPA). Also, this study determined the reliability of free-living sitting and MVPA time as it useful for guiding researchers in determining how many days of monitoring are needed.An activPAL monitor was worn for 7 consecutive days by 68 women (52±8 years).Intra-individual range of daily sitting time was calculated. Generalizability theory analysis determined the reliability of daily sitting and recommended MVPA.Mean sitting time was 9.0±1.8h/day and the within individual weekly mean range was 4.5±1.7h/day. Similarly, there was a 4.5h/day difference in sitting time between the mean of the lowest sitting (6.7±0.8) and highest sitting (11.3±1.1h/day) quartiles. The intra-individual range in daily sitting did not differ among quartiles of sitting time (i.e., 4.9±1.9, 4.1±1.9, 5.1±1.5, 3.9±1.1h/day for the 1st-4th quartiles) nor among quartiles of MVPA (i.e., 4.2±1.8, 4.7±2.0, 4.6±1.5, 4.4±1.3h/day for the 1st-4th quartiles). A reliability coefficient of 0.80 was achieved with 4 days of objectively measured sitting time and 7 days for MVPA.The findings suggest exposure to relatively high levels of sedentary time may occur in people regardless of weekly averages in sitting and regular exercise due to the high day-to-day variation in daily sitting time (4.5h/d range within a week).

| S-EPMC4655191 | biostudies-literature

Intra- and inter-individual genetic differences in gene expression.

Project description:Genetic variation is known to influence the amount of mRNA produced by a gene. Because molecular machines control mRNA levels of multiple genes, we expect genetic variation in components of these machines would influence multiple genes in a similar fashion. We show that this assumption is correct by using correlation of mRNA levels measured from multiple tissues in mouse strain panels to detect shared genetic influences. These correlating groups of genes (CGGs) have collective properties that on average account for 52-79% of the variability of their constituent genes and can contain genes that encode functionally related proteins. We show that the genetic influences are essentially tissue-specific and, consequently, the same genetic variations in one animal may upregulate a CGG in one tissue but downregulate the CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. Thus, this class of genetic variation can result in complex inter- and intraindividual differences. This will create substantial challenges in humans, where multiple tissues are not readily available.

| S-EPMC2690833 | biostudies-literature

Large inter-individual and intra-individual variability in the effect of perceptual load.

Project description:This study examined whether the recurrent difficulty to replicate results obtained with paradigms measuring distractor processing as a function of perceptual load is due to individual differences. We first reanalyzed, at the individual level, the data of eight previously reported experiments. These reanalyses revealed substantial inter-individual differences, with particularly low percentage of participants whose performance matched the load theory's predictions (i.e., larger distractor interference with low than high levels of load). Moreover, frequently the results were opposite to the theory's predictions-larger interference in the high than low load condition; and often a reversed compatibility effect emerged-better performance in the incompatible than neutral condition. Subsequently, seven observers participated in five identical experimental sessions. If the observed inter-individual differences are due to some stable trait or perceptual capacity, similar results should have emerged in all sessions of a given participant. However, all seven participants showed large between-sessions variations with similar patterns to those found between participants. These findings question the theoretical foundation implemented with these paradigms, as none of the theories suggested thus far can account for such inter- and intra-individual differences. Thus, these paradigms should be used with caution until further research will provide better understanding of what they actually measure.

| S-EPMC5391011 | biostudies-literature

Intra- and inter-individual differences in human sperm DNA methylation.

Project description:There is growing evidence that sperm DNA methylation is important in maintaining proper sperm health and function. Previous studies have associated sperm DNA methylation levels with sperm quality and function, however, little is known regarding the intra- and inter-individual variability in sperm methylation levels. This study characterizes this variation. Sperm epigenetic differences between successive semen samples from 12 patients were examined to identify the intra- and inter-individual differences globally across the genome, and in specifically defined genomic regions using the Illumina Infinium HumanMethylation450 BeadChips. Methylation analysis identified a bimodal distribution in the methylation levels that were non-uniformly distributed across the different genomic regions. The methylation levels were highly correlated in both the intra- and inter-individual comparisons. The intra-individual methylation levels were more highly correlated than the inter-individual comparison both globally and across the defined genomic regions, demonstrating that sperm DNA methylation levels are relatively stable between semen sample collections.

| S-EPMC4988918 | biostudies-literature

Intra- and inter-individual genetic differences in gene expression (BXD Brain)

Project description:Genetic variation is known to influence the amount of mRNA produced by a gene. Because molecular machines control mRNA levels of multiple genes, we expect genetic variation in components of these machines would influence multiple genes in a similar fashion. We show that this assumption is correct by using correlation of mRNA levels measured from multiple tissues in mouse strain panels to detect shared genetic influences. These correlating groups of genes (CGGs) have collective properties that on average account for 52–79% of the variability of their constituent genes and can contain genes that encode functionally related proteins. We show that the genetic influences are essentially tissue-specific and, consequently, the same genetic variations in one animal may upregulate a CGG in one tissue but downregulate the CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. Thus, this class of genetic variation can result in complex inter- and intra-individual differences. This will create substantial challenges in humans, where multiple tissues are not readily available.

2009-05-19 | GSE8355 | GEO

Evaluating intra- and inter-individual variation in the human placental transcriptome

Project description:Background: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. Results: We estimate that on average, 33.2%, 58.9% and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling and metabolism. Many biological traits demonstrated correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome (65% of expressed genes) exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection (26%), directional selection (4.9%), or diversifying selection (4.8%). Conclusion: We apportion placental gene expression variation into individual, population and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

2015-03-07 | GSE66622 | GEO

Intra- and inter-individual genetic differences in gene expression (BXD Kidney)

Project description:Genetic variation is known to influence the amount of mRNA produced by a gene. Because molecular machines control mRNA levels of multiple genes, we expect genetic variation in components of these machines would influence multiple genes in a similar fashion. We show that this assumption is correct by using correlation of mRNA levels measured from multiple tissues in mouse strain panels to detect shared genetic influences. These correlating groups of genes (CGGs) have collective properties that on average account for 52–79% of the variability of their constituent genes and can contain genes that encode functionally related proteins. We show that the genetic influences are essentially tissue-specific and, consequently, the same genetic variations in one animal may upregulate a CGG in one tissue but downregulate the CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. Thus, this class of genetic variation can result in complex inter- and intra-individual differences. This will create substantial challenges in humans, where multiple tissues are not readily available.

2009-05-19 | GSE8356 | GEO

Intra- and Inter-Individual Variance of Gene Expression in Human Placenta

Project description:Variance in microarray studies has been widely discussed as a critical topic of the identification of differentially expressed gene; however, few studies have addressed the influence of estimating variance. To break intra- and inter-individual variance in clinical studies down to three levels: technical, anatomic, and individual, we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of “inter-individual variable genes” were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduce/eliminate the effects of underestimated variance. Our data demonstrates that an appropriate evaluation of variance is critical in selecting significant genes of differential expression. If the estimation of precise variance has not been adequately considered in the experimental design, using a higher fold change criteria is one possible solution to overcome the difficulties associated with the identification of significant genes, but it paid by losing the number of selected genes.

2011-03-02 | GSE27646 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data