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PXD001406 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleImpact of Regulatory Variation from RNA to Protein
DescriptionGenetic 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 phenotypic consequences of eQTLs are presumably due, in most cases, to their ultimate effects on protein expression levels. Yet, only few studies have quantified the impact of genetic variation on proteins levels directly. It remains unclear how faithfully eQTLs are reflected at the protein level, and whether there is a significant layer of cis regulatory variation acting primarily on translation or steady state protein levels. To address these questions, we measured ribosome occupancy by high-throughput sequencing, and relative protein levels by high-resolution quantitative mass spectrometry, in a panel of lymphoblastoid cell lines (LCLs) in which we had previously measured transcript expression using RNA sequencing. We then mapped genetic variants that are associated with changes in transcript expression (eQTLs), ribosome occupancy (rQTLs), or protein abundance (pQTLs). Most of the QTLs we detected are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, we found that eQTLs tend to have significantly reduced effect sizes on protein levels, suggesting that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we confirmed the presence of a class of cis QTLs that specifically affect protein abundance with little or no effect on mRNA levels; most of these QTLs have little effect on ribosome occupancy, and hence may arise from differences in post-translational regulation.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterZia Khan
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-10-17 00:22:07ID requested
12014-12-19 06:55:53announced
22017-06-20 05:42:58announcedUpdated project metadata.
Publication List
Dataset with its publication pending
Keyword List
curator keyword: Biological
submitter keyword: SILAC, genetic variation, HapMap, lymphoblastoid cell line, Ribosome profiling, RNA-seq, pQTL, eQTL, post-translational, gene regulation
Contact List
Yoav Gilad
contact affiliationDepartment of Human Genetics University of Chicago
contact emailgilad@uchicago.edu
lab head
Zia Khan
contact affiliationUniversity of Maryland College Park Center for Bioinformatics and Computational Biology Department of Computer Science
contact emailzia@cs.umd.edu
dataset submitter
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Dataset FTP location
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