Genome-wide analysis of gene expression profiles in the Rotterdam Study III
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE33828 | GEO | 2013/05/31
SECONDARY ACCESSION(S): PRJNA148201
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiles were compared to investigate age-marking differential gene expression. We obtained Whole blood RNA of 881 participants of the Rotterdam Study III.
2013-05-31 | E-GEOD-33828 | biostudies-arrayexpress
Project description:Biomarkers of familial longevity may represent mechanisms underlying healthy aging. To identify gene expression profiles marking human familial longevity, an explorative genome-wide expression study was performed among 50 families from the Leiden Longevity Study who have a life-long survival advantage of 30%. Gene expression profiles were compared between 50 nonagenarians (mean age 93.4 years) and 50 controls (mean age 61.9 years) to investigate differential gene expression that may arise as a function of both chronological age and familial longevity. Differential expression was observed for 2953 probes (FDR≤0.05) and for 109 GO terms, which corresponded well with previously reported findings on gene expression changes associated with chronological age, such as ‘immune response’, ‘signal transduction’ and ‘regulation of gene transcription’. To explore which of the 2953 chronological age-related probes also marked familial longevity, we compared gene expression profiles of 50 offspring of the nonagenarians (mean age 60.8 years) with the same 50 controls. Since the average gene expression levels did not differ between offspring and controls, we tested for differential expression as a function of age (age range 43-79 years). We identified 360 probes (FDR≤0.1) and the ‘Rho protein signal transduction’ GO biological process (FWER = 0.079) whose expression signatures marked familial longevity already at middle-age. Of these probes, 236 were annotated and represent 244 known genes, including WRN and MYC. Interestingly, 51 genes are involved in the regulation of gene expression. Further investigation into the genes involved may be important for unraveling mechanisms underlying longevity.
2011-09-04 | GSE16717 | GEO
Project description:In order to investigate age-correlated DNA methylation changes in saliva, genome-wide DNA methylation profiling was performed for saliva from 54 males aged 18 to 73 years. The Illumina Infinium 450k Human DNA methylation Beadchip was used to acquire DNA methylation profiles across about 450,000 CpGs in bisulfite converted DNA.
2017-04-02 | GSE92767 | GEO
Project description:Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics. In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification.A single molecule approach is presented for the discernment of methylation profiles, based on optical mapping. We report results from a series of pilot studies demonstrating the capabilities of optical mapping as a platform for methylation profiling of whole genomes. Optical mapping was used to discern the methylation profile from both an engineered and wild type Escherichia coli. Furthermore, the methylation status of selected loci within the genome of human embryonic stem cells was profiled using optical mapping.The optical mapping platform effectively detects DNA methylation patterns. Due to single molecule detection, optical mapping offers significant advantages over other technologies. This advantage stems from obviation of DNA modification steps, such as bisulfite treatment, and the ability of the platform to assay repeat dense regions within mammalian genomes inaccessible to techniques using array-hybridization technologies.
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Project description:The average age of fatherhood has increased in recent years. Various genetic diseases are also known to be more likely in children with older fathers. This leads to a need to investigate age-related changes to the sperm DNA. The sperm methylome can be used to accurately predict fertility and embryo viability, and it also changes continuously with age. To date, most population studies that investigate age-related changes to the sperm methylome use microarrays, which are less expensive but, compared to sequencing-based approaches, investigate the methylome at much lower spatial resolution.
2023-03-01 | GSE222340 | GEO
Project description:IntroductionPlant-specific Class III peroxidases (PRXs) play a crucial role in lignification, cell elongation, seed germination, and biotic and abiotic stresses.MethodsThe class III peroxidase gene family in sugarcane were identified by bioinformatics methods and realtime fluorescence quantitative PCR.ResultsEighty-two PRX proteins were characterized with a conserved PRX domain as members of the class III PRX gene family in R570 STP. The ShPRX family genes were divided into six groups by the phylogenetic analysis of sugarcane, Saccharum spontaneum, sorghum, rice, and Arabidopsis thaliana. The analysis of promoter cis-acting elements revealed that most ShPRX family genes contained cis-acting regulatory elements involved in ABA, MeJA, light responsiveness, anaerobic induction, and drought inducibility. An evolutionary analysis indicated that ShPRXs was formed after Poaceae and Bromeliaceae diverged, and tandem duplication events played a critical role in the expansion of ShPRX genes of sugarcane. Purifying selection maintained the function of ShPRX proteins. SsPRX genes were differentially expressed in stems and leaves at different growth stages in S. spontaneum. However, ShPRX genes were differentially expressed in the SCMV-inoculated sugarcane plants. A qRT-PCR analysis showed that SCMV, Cd, and salt could specifically induce the expression of PRX genes of sugarcane.DiscussionThese results help elucidate the structure, evolution, and functions of the class III PRX gene family in sugarcane and provide ideas for the phytoremediation of Cd-contaminated soil and breeding new sugarcane varieties resistant to sugarcane mosaic disease, salt, and Cd stresses.
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Project description:Differential DNA methylation was identified in CdLS, and correlates to cohesin binding as well. However, DNA methylation may only be one of several events that regulate gene expression in humans.
2010-07-07 | GSE18458 | GEO
Project description:BACKGROUND: With the availability of large-scale genome-wide association study (GWAS) data, choosing an optimal set of SNPs for disease susceptibility prediction is a challenging task. This study aimed to use single nucleotide polymorphisms (SNPs) to predict psoriasis from searching GWAS data. METHODS: Totally we had 2,798 samples and 451,724 SNPs. Process for searching a set of SNPs to predict susceptibility for psoriasis consisted of two steps. The first one was to search top 1,000 SNPs with high accuracy for prediction of psoriasis from GWAS dataset. The second one was to search for an optimal SNP subset for predicting psoriasis. The sequential information bottleneck (sIB) method was compared with classical linear discriminant analysis(LDA) for classification performance. RESULTS: The best test harmonic mean of sensitivity and specificity for predicting psoriasis by sIB was 0.674(95% CI: 0.650-0.698), while only 0.520(95% CI: 0.472-0.524) was reported for predicting disease by LDA. Our results indicate that the new classifier sIB performs better than LDA in the study. CONCLUSIONS: The fact that a small set of SNPs can predict disease status with average accuracy of 68% makes it possible to use SNP data for psoriasis prediction.
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Project description:This SuperSeries is composed of the following subset Series: GSE31233: Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation that establish T cell identity [ChIP-Seq] GSE31234: Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation that establish T cell identity [RNA-Seq] Refer to individual Series
2012-04-13 | E-GEOD-31235 | biostudies-arrayexpress