Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of CEPH individuals from the International HapMap Project

ABSTRACT: Baseline expression levels of genes in CEPH individuals from the International HapMap Project were measured using the Affymetrix Human Genome Focus Arrays. Arrays were analyzed using MAS 5.0 software (Affymetrix).

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Morley

PROVIDER: E-GEOD-2552 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Mapping determinants of human gene expression by regional and genome-wide association.

Cheung Vivian G VG Spielman Richard S RS Ewens Kathryn G KG Weber Teresa M TM Morley Michael M Burdick Joshua T JT

Nature 20051001 7063

To study the genetic basis of natural variation in gene expression, we previously carried out genome-wide linkage analysis and mapped the determinants of approximately 1,000 expression phenotypes. In the present study, we carried out association analysis with dense sets of single-nucleotide polymorphism (SNP) markers from the International HapMap Project. For 374 phenotypes, the association study was performed with markers only from regions with strong linkage evidence; these regions all mapped ...[more]

PMID: 16251966

Similar Datasets

Homo sapiens strain:(CEU) CEPH HapMap population

Project description:Exome sequencing of (CEU) Utah residents with ancestry from Northern and Western Europe - CEPH - HapMap population

| PRJNA59853 | ENA

A type 2C protein phosphatase activates high-affinity nitrate uptake by directly dephosphorylating NRT2.1 in Arabidopsis

Project description:Nitrate transporter NRT2.1, which plays a central role in high-affinity nitrate uptake in roots, is activated at the post-translational level in response to nitrogen (N) starvation. However, critical enzymes required for post-translational activation of NRT2.1 remain to be identified. Here, we show that a type 2C protein phosphatase, designated CEPD-induced phosphatase (CEPH), activates high-affinity nitrate uptake by directly dephosphorylating S501 of NRT2.1, a residue that functions as a negative phospho-switch. CEPH is predominantly expressed in epidermal and cortex cells in roots and up-regulated by N starvation via a CEPDL2/CEPD1/2-mediated long-distance signaling from shoots. Loss of CEPH leads to a marked decrease in high-affinity nitrate uptake, tissue nitrate content, and plant biomass. Collectively, our results identify CEPH as a crucial enzyme in N starvation-dependent activation of NRT2.1, providing molecular and mechanistic insights into how plants regulate high-affinity nitrate uptake at the post-translational level in response to the N environment.

2021-03-02 | PXD022343 | Pride

Homo sapiens strain:(CEU) CEPH HapMap population

Project description:Whole genome sequencing of (CEU) Utah residents with ancestry from Northern and Western Europe - CEPH - HapMap population

| PRJNA33831 | ENA

International HapMap Project

Project description:A haplotype map (HapMap) of the human genome.

| PRJNA60817 | ENA

HapMap Yoruban individuals vs CEPH reference

Project description:It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. We identified a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the parent-offspring trios. This new method will permit future identification of deletion polymorphisms from high density SNP data derived from parent-offspring trios or other family relationships. Keywords: comparative genomic hybridisation

2005-11-17 | GSE3474 | GEO

Custom array CGH validation of de novo CNVs in CEU HapMap samples

Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459.

2010-09-01 | GSE23575 | GEO

Custom array CGH validation of de novo CNVs in CEU HapMap samples

2010-09-01 | E-GEOD-23575 | biostudies-arrayexpress

HapMap CEU parent custom array expression

Project description:The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe (CEPH) using the publicly available phase I data of the International HapMap project. The genes are located in regions of the human genome with elevated functional annotation and disease interest including the ENCODE regions spanning 1% of the genome, chromosome 21 and chromosome 20q12-13.2. We apply three different methods of multiple test correction, including Bonferroni, False Discovery Rate and permutations. For the 374 expressed genes, we find many regions with statistically significant association of SNPs with expression variation in lymphoblastoid cell lines after correcting for multiple tests. Based on our analyses, the signal proximal (cis-) to the genes of interest is more abundant and more stable than distal and trans across statistical methodologies. Our results suggest that regulatory polymorphism is widespread in the human genome and show that the 5 kb (phase I) HapMap has sufficient density to enable linkage disequilibrium mapping in humans. Such studies will significantly enhance our ability to annotate the non-coding part of the genome and interpret functional variation. In addition, we demonstrate that the HapMap cell lines themselves may serve as a useful resource for quantitative measurements at the cellular level. Keywords: Gene expression, Lymphoblastoid,

2005-12-01 | GSE3612 | GEO

Genotyping of human lymphoblastoid cell lines from pairs of HapMap indiviudals pooled in varying proportions using Illumina GoldenGate SNP arrays

Project description:In this experiment genomic DNA samples from lymphoblastoid cell lines from pairs of HapMap indiviudals were pooled in varying proportions. This design produces predictable changes in allelic imbalance for all SNPs which differ between individuals. The mixtures were hybridized to Illumina GoldenGate SNP arrays.

2010-03-30 | E-TABM-855 | biostudies-arrayexpress

Illumina HapMap (550duo)

Project description:HapMap samples

2009-07-27 | GSE16912 | GEO