HAPMAP3_EXPRESSION
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Stephen Stephen Montgomery
PROVIDER: E-MTAB-264 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Array quantification of 112 HapMap CEU individuals, 60 supporting RNA-seq of the same individuals, 109 supporting HapMap3 analysis
2010-06-01 | E-MTAB-198 | biostudies-arrayexpress
Project description:Expression level of genes in lymphoblasts from individuals in three HapMap populations (CEU, CHB, JPT) were compared. More than 1,000 genes were found to be significantly different (Pc<0.05) in mean expression level between the CEU and CHB+JPT samples. Keywords: Comparison of Gene Expression Profiles from Lymphoblastoid cells
2007-01-07 | GSE5859 | GEO
Project description:In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations. Exon level expression on 176 HapMap cell lines.
2010-08-19 | E-GEOD-9703 | biostudies-arrayexpress
Project description:In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations.
2009-03-23 | GSE9703 | GEO
Project description:Elucidating cytosine modification difference between human populations can enhance our understanding of ethnic specificity in complex traits such as disease predisposition and drug response. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines (LCLs) derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at false discovery rate (FDR) of 1%. CpG sites with greater modification levels in European descents were enriched in the proximal regulatory regions, while those greater in African descents were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained by genetic variation. A substantial proportion of local modification quantitative trait loci (mQTL) exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interaction could be common. Distinct inter-individual correlations were observed between gene expression and cytosine modifications in both proximal promoters and gene bodies, demonstrating a regulatory role of inter-individual variation in cytosine modification. Furthermore, a number of SNPs (single nucleotide polymorphisms) previously identified for complex traits with known racial disparities could be annotated as mQTLs for population-specific CpGs. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression. 60 HapMap CEU and 73 HapMap YRI samples from Coriell Insitute were profiled for cytosine modification levels.
2013-07-01 | E-GEOD-39672 | biostudies-arrayexpress
Project description:RNA-sequencing of 60 HapMap CEU individuals
2010-06-01 | E-MTAB-197 | biostudies-arrayexpress
Project description:Expression level of genes in lymphoblasts from individuals in three HapMap populations (CEU, CHB, JPT) were compared. More than 1,000 genes were found to be significantly different (Pc<0.05) in mean expression level between the CEU and CHB+JPT samples. Experiment Overall Design: Gene expression analysis using Affymetrix Human Focus arrays; comparison of expression levels of genes by t-test.
2008-06-14 | E-GEOD-5859 | biostudies-arrayexpress
Project description:B lymphoblastoid cell lines were obtained from Coriell Cell Repositories. Cell lines were grown according to Coriell guidelines and total RNA was extracted, labeled, and hybridized to an Affymetrix Human Genome Focus Array as previously described. We found extensive variation in gene-expression levels and estimate that ~83% of genes are differentially expressed among individuals and that ~17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation. Experiment Overall Design: We used microarrays to survey patterns of natural gene expression variation in 16 HapMap individuals derived from the CEU and YRI samples.
2008-06-15 | E-GEOD-7236 | biostudies-arrayexpress
Project description:Discovery of common Asian copy number variants using a novel integrated high-resolution array CGH and massively parallel DNA sequencing. We attempted to discover common Asian copy number variants (CNVs) from the DNA of 30 Asian women (10 Korean, 10 CHB (HapMap), 10 JPT (HapMap)) using a custom-designed 24M-oligonucleotide Agilent platform (1.1M X 24 slides). The reference sample for aCGH was NA10851 (HapMap CEPH). In addition to the 30 women, 3 more individuals were analyzed as controls (AK1 (Kim, J.I. et al., 2009 Nature), NA12878 and NA19240).
2010-01-13 | GSE19651 | GEO