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ProteomicsA Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Phosphorylation of proteins on serine, threonine, and tyrosine residues is a ubiquitous post-translational modification that plays a key part of essentially every cell signaling process. It is reasonable to assume that inter-individual variation in protein phosphorylation may underlie phenotypic dif...
ORGANISM(S): Homo sapiens (Human) 
2018-10-22 | PXD008002 | Pride
Human Maxquant Lcl Yri Lc-ms/ms 
ProteomicsImpact of Regulatory Variation from RNA to Protein
Genetic variants that impact gene regulation are important contributors to human phenotypic variation. For this reason, considerable efforts have been made to identify genetic associations with differences in mRNA levels of nearby genes, namely, cis expression quantitative trait loci (eQTLs). The ph...
ORGANISM(S): Homo sapiens (Human) 
2014-12-19 | PXD001406 | Pride
Post-translational Ribosome profiling Eqtl Gene regulation Hapmap Silac Genetic variation Lymphoblastoid cell line Pqtl Rna-seq 
TranscriptomicsPrimate Comparison Study
Comparing different primates to Human; treated vs.untreated
ORGANISM(S): Pongo pygmaeus 
2010-06-11 | E-GEOD-2569 | biostudies-arrayexpress
GenomicsGene expression differences among primates are associated with changes in a histone epigenetic modification
Changes in gene regulation are thought to play an important role in speciation and adaptation, especially in primates. However, we still know relatively little about the mechanisms underlying regulatory evolution. In particular, the extent to which epigenetic modifications underlie gene expression d...
ORGANISM(S): Homo sapiens 
2011-02-15 | E-GEOD-24111 | biostudies-arrayexpress
TranscriptomicsEffect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here we investigate the impact of SNP variation on the reliab...
ORGANISM(S): Homo sapiens 
2009-10-22 | E-GEOD-18156 | biostudies-arrayexpress
TranscriptomicsExpression data from kidney and liver of an adult human male
mRNA expression differences between the liver and kidney of an adult male (homo sapien) were investigated using three technical replicates. The purpose of the experiment was to compare array data generated using Affymetrix with measures of expression obtained using RNAseq (a sequencing approach for ...
ORGANISM(S): Homo sapiens 
2008-06-01 | E-GEOD-11045 | biostudies-arrayexpress
Transcriptomics4sUDRB-seq: measuring transcription elongation and initiation genomewide
A new method to measure elongation and intitiation rates Reversal inhibition of transcription with DRB and tagging newly transcribed RNA with 4-thiouridine (4sU)
ORGANISM(S): Homo sapiens 
2014-05-09 | E-GEOD-57116 | biostudies-arrayexpress
GenomicsDramatic effects of social behavior on gene regulation in rhesus macaques [Bisulfite seq]
These data are a component of a larger study investigating differences in gene regulation in relationship to rhesus macaque dominance rank. These data compare DNA methylation levels between individuals of different rank on a genome-wide scale using bisulfite sequencing DNA from peripheral blood mono...
ORGANISM(S): Macaca mulatta 
2012-02-01 | E-GEOD-34128 | biostudies-arrayexpress
TranscriptomicsUnderstaning mechanisms underlying human gene expression variation with RNA sequencing
Understanding the genetic mechanisms underlying natural variation in gene expression is a central goal of both medical and evolutionary genetics, and studies of expression quantitative trait loci (eQTLs) have become an important tool for achieving this goal. While all eQTL studies to date have assay...
ORGANISM(S): Homo sapiens 
2010-02-28 | E-GEOD-19480 | biostudies-arrayexpress
TranscriptomicsGenome-wide inter-primate comparison of gene expression profiles in multiple tissues
Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes whose regulation evolves under natural selection. To do so, we used a novel multi-species microarray to measur...
ORGANISM(S): Macaca mulatta 
2008-09-17 | E-GEOD-11560 | biostudies-arrayexpress
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