Phenotype
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PROVIDER: EGAD00010001729 | EGA |
REPOSITORIES: EGA
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Project description:Individual differences in basal leukocyte gene expression profiles as a function of child's and parent's perception of family stress, and as a function of parent's psychological well-being. Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 273 individuals (129 parent:child pairs + 15 parent-or-child) who were also assessed on their perceptions of family stress (both parent's and child's perception). Each dyad is labeled by a case ID, with p suffix indicating parent's gene expression profile and c suffix indicating child's gene expression profile. Variations in gene expression are analyzed as a function of both parent's perception of family stress and child's perception of family stress (using UCLA Life Stress Interview, as previously described: Hammen C (1991) Generation of stress in the course of unipolar depression. J Abnorm Psychol 100:555-561; Adrian C, Hammen C (1993) Stress Exposure and Stress Generation in Children of Depressed Mothers. Journal of Consulting and Clinical Psychology 61:354-359; Rudolph KD, Hammen C (1999) Age and gender as determinants of stress exposure, generation, and reactions in youngsters: A transactional perspective. Child Development 70:660-677). Higher values indicate greater levels of subjectively perceived family stress. Additional data are available for 107 parents who completed all 6 subscales of the Psychological Well-Being (PWB) Scale (Ryff CD (1989) Happiness is everything, or is it? Explorations on the meaning of psychological well-being. J. Pers Soc. Psychol 57: 1069-1081), resulting in scores for PWB_Total (average score across all 6 subscales) as well as scores for subscales measuring Purpose in Life (PWB_Purpose), Environmental Mastery (PWB_Environmental_Mastery), Self-Acceptance (PWB_Self_Accept), Autonomy (PWB_Autonomy), Personal Growth (PWB_Growth), Positive Relations with Others (PWB_Relationship). Higher scores indicate greater psychological well being. Also available for those individuals are measures of age (years), male gender (0/1), ethnic group (1=White, 2=Chinese, 3=Indian, 4=Other Asian, 5=Other Ethnicity), Body Mass Index (kg/m^2), heavy alcohol consumption history (0/1), smoking history (0/1), and abundance of 8 mRNA transcripts indicating the relative prevalence of major leukocyte subsets (CD3E, CD3D, CD19, CD4, CD8A, FCGR3A, NCAM1, CD14). key word: Risk prediction
2015-03-28 | E-GEOD-45329 | biostudies-arrayexpress
Project description:DOWNREGULATION OF SPLICING REGULATOR RBFOX1 COMPROMISES VISUAL DEPTH PERCEPTION
| PRJNA414610 | ENA
Project description:The sensation of light is initiated in photoreceptor cells by the photoisomerization of a chromophore molecule from 11-cis to all-trans retinal. Continuous visual perception requires recycling of the spent chromophore back to the 11-cis form through the visual cycle, a series of reactions in the retinal pigmented epithelium (RPE). Light-driven chromophore consumption by photoreceptors is greater in daytime compared to night time, suggesting that correspondingly higher activity of the visual cycle may be required. On the other hand, as rod photoreceptors are saturated in bright light, the continuous turnover of their chromophore through the visual cycle during daytime would unnecessarily utilize precious energy and produce toxic byproducts. Here, we sought to determine whether the recycling of chromophore and the dark adaptation of rods is regulated by the circadian clock and light exposure. We demonstrate that in melatonin-proficient C3H/f+/+ mice, rod dark adaptation is slower during the day or after light exposure. This surprising daytime downregulation of the RPE visual cycle was further demonstrated by gene analysis, which revealed light-driven reduction in the expression of Rpe65, which encodes a key enzyme of the RPE visual cycle. In contrast, rods in melatonin-deficient strains (C57BL6/J and 129/Sv) were not affected by this daily visual cycle modulation. Our results demonstrate that the circadian clock and light exposure regulate the recycling of chromophore in the RPE visual cycle. This daily modulation of rod dark adaptation is mediated by melatonin and could potentially protect the retina from light-induced damage during the day. mRNA-seq of murine eyes (lens removed) in objective day (OD) vs. subjective day (SD) conditions (2 biological replicates per condition). Each biological replicate consisted of 4 eyes (from 1 female and 1 male).
2015-11-19 | E-GEOD-68470 | biostudies-arrayexpress
Project description:Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave- one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5× and higher compared to the Illumina GSA.
2021-01-31 | GSE165845 | GEO
Project description:The sensation of light is initiated in photoreceptor cells by the photoisomerization of a chromophore molecule from 11-cis to all-trans retinal. Continuous visual perception requires recycling of the spent chromophore back to the 11-cis form through the visual cycle, a series of reactions in the retinal pigmented epithelium (RPE). Light-driven chromophore consumption by photoreceptors is greater in daytime compared to night time, suggesting that correspondingly higher activity of the visual cycle may be required. On the other hand, as rod photoreceptors are saturated in bright light, the continuous turnover of their chromophore through the visual cycle during daytime would unnecessarily utilize precious energy and produce toxic byproducts. Here, we sought to determine whether the recycling of chromophore and the dark adaptation of rods is regulated by the circadian clock and light exposure. We demonstrate that in melatonin-proficient C3H/f+/+ mice, rod dark adaptation is slower during the day or after light exposure. This surprising daytime downregulation of the RPE visual cycle was further demonstrated by gene analysis, which revealed light-driven reduction in the expression of Rpe65, which encodes a key enzyme of the RPE visual cycle. In contrast, rods in melatonin-deficient strains (C57BL6/J and 129/Sv) were not affected by this daily visual cycle modulation. Our results demonstrate that the circadian clock and light exposure regulate the recycling of chromophore in the RPE visual cycle. This daily modulation of rod dark adaptation is mediated by melatonin and could potentially protect the retina from light-induced damage during the day.
2015-11-19 | GSE68470 | GEO
Project description:We identified 737 differentially expressed genes, including 430 upregulated genes and 307 downregulated genes, by calculating the gene FPKM in each sample and conducting differential gene analysis. Gene ontology analysis and KEGG pathway enrichment analysis suggested that blue light influenced visual perception, sensory perception of light stimulus, phototransduction, and JAK-STAT signaling pathways. Differential lncRNA, circRNA and miRNA analysis suggested that blue light exposure affected pathways for retinal cone cell development and phototransduction, among others.
2020-08-24 | GSE149549 | GEO
Project description:Gene expression profiles were generated from muscle biopsies from 134 individuals, and differences in expression based on sex were explored. Top differentially expressed gene lists are often inconsistent between studies and it has been suggested that small sample sizes contribute to lack of reproducibility and poor prediction accuracy in discriminative models. We considered sex differences (69♂, 65♀) in 134 human skeletal muscle biopsies using DNA microarray. The full dataset and subsamples (n= 10 (5♂, 5♀) to n=120 (60♂, 60♀)) thereof were used to assess the effect of sample size on the differential expression of single genes, gene rank order and prediction accuracy. Using our full dataset (n=134), we identified 717 differentially expressed transcripts (p-value < 0.0001; false discovery rate < 0.006) and we were able to predict sex with 92% accuracy, both within our dataset and on external datasets. Both p-values and rank order of top differentially expressed genes became more variable using smaller subsamples. For example, at n=10 (5♂, 5♀), no gene was considered differentially expressed at p<0.0001 and prediction accuracy was ~50% (no better than chance). We found that sample size clearly affects microarray analysis results; small sample sizes result in unstable gene lists and poor prediction accuracy. We anticipate this will apply to other phenotypes, in addition to sex.
2014-05-15 | GSE41726 | GEO
Project description:Visual deprivation, either in the form of dark rearing (DR) or monocular deprivation (MD) are established paradigms for studying cortical plasticity. We have used miRNA microarray to uncover miRNAs whose expression is altered in primary visual cortex following DR and/or MD.
2011-09-04 | GSE31536 | GEO
Project description:Gene expression profiles were generated from muscle biopsies from 134 individuals, and differences in expression based on sex were explored. Top differentially expressed gene lists are often inconsistent between studies and it has been suggested that small sample sizes contribute to lack of reproducibility and poor prediction accuracy in discriminative models. We considered sex differences (69M-bM-^YM-^B, 65M-bM-^YM-^@) in 134 human skeletal muscle biopsies using DNA microarray. The full dataset and subsamples (n= 10 (5M-bM-^YM-^B, 5M-bM-^YM-^@) to n=120 (60M-bM-^YM-^B, 60M-bM-^YM-^@)) thereof were used to assess the effect of sample size on the differential expression of single genes, gene rank order and prediction accuracy. Using our full dataset (n=134), we identified 717 differentially expressed transcripts (p-value < 0.0001; false discovery rate < 0.006) and we were able to predict sex with 92% accuracy, both within our dataset and on external datasets. Both p-values and rank order of top differentially expressed genes became more variable using smaller subsamples. For example, at n=10 (5M-bM-^YM-^B, 5M-bM-^YM-^@), no gene was considered differentially expressed at p<0.0001 and prediction accuracy was ~50% (no better than chance). We found that sample size clearly affects microarray analysis results; small sample sizes result in unstable gene lists and poor prediction accuracy. We anticipate this will apply to other phenotypes, in addition to sex. RNA was isolated from 134 muscle samples. Gene expression is compared between males and females.
2014-05-15 | E-GEOD-41726 | biostudies-arrayexpress
Project description:Histologic diagnosis of T cell-mediated rejection in kidney transplant biopsies has limited reproducibility because it is based on non-specific lesions using arbitrary rules that are subject to differing interpretations. We used microarray results from 403 indication biopsies previously given histologic diagnoses to develop a molecular classifier that assigned a molecular T cell-mediated rejection score to each biopsy. Independent assessment of the biopsies by multiple pathologists confirmed considerable disagreement on the presence of TCMR features: 79-88% accuracy and 35-69% sensitivity. The agreement of the molecular T cell-mediated rejection score with the histology diagnosis was similar to agreement among individual pathologists: accuracy 89%, sensitivity 51%. However, the score also predicted the consensus among pathologists, being highest when all agreed. Many discrepancies between the scores and the histologic diagnoses were in situations where histology is unreliable e.g. scarred biopsies. The score correlated with histologic lesions and gene sets associated with T cell-mediated rejection. The transcripts most often selected by the classifier were expressed in effector T cells, dendritic cells, or macrophages or inducible by interferon-gamma. Thus the T cell-mediated rejection score offers an objective assessment of kidney transplant biopsies, predicting the consensus opinion among multiple pathologists, and offering insights into underlying disease mechanisms. Antibody-mediated rejection is a major cause of kidney transplant failure, but the current diagnostic system misses most cases due to dependency on subjective non-standardized tests. We hypothesized that molecular features could provide a test to address this problem. We classified 403 biopsies by a reference standard based on microcirculation lesions and donor-specific HLA antibody, and used microarray analysis to develop a classifier that assigned each biopsy a score reflecting the probability of antibody-mediated rejection. The scores correlated with donor-specific antibody and histologic lesions: 42/45 biopsies with antibody-mediated rejection scores >0.5 had both donor-specific antibody and microcirculation lesions. Intermediate scores (0.2-0.5) were more ambiguous, but became more specific combined with donor-specific antibody. Compared to diagnoses based on histology-plus-donor-specific antibody, the scores had sensitivity 0.67; specificity 0.90. Donor-specific antibody improved the specificity to 0.97. The score correlated not only with diagnoses of individual pathologists but with the consensus among multiple pathologists. The classifier used transcripts expressed in endothelial cells (e.g. CDH13, DARC, ROBO4) and NK cells (e.g. CX3CR1, FGFBP2), as well as IFNG-inducible transcripts e.g. CXCL11. Thus the molecular phenotype of antibody-mediated rejection provides not only an objective test that predicts microcirculation lesions and donor-specific HLA antibody, but also offers mechanistic insights. All consenting renal transplant patients undergoing biopsies for cause as standard of care. 403 samples and 8 controls (nephrectomies). This dataset is part of the TransQST collection.
2013-02-13 | E-GEOD-36059 | biostudies-arrayexpress