PXD019169

PXD019169 is an original dataset announced via ProteomeXchange.

Title	Genome-wide pQTL analysis of protein expression regulatory networks in the human liver
Description	Background: Previous expression quantitative trait loci (eQTL) studies have identified thousands of genetic variants to be associated with gene expression at the mRNA level in the human liver. However, protein expression often correlates poorly with mRNA levels. Thus, protein quantitative trait loci (pQTL) study is required to identify genetics variants that regulate protein expression in human livers. Results: We conducted a genome-wide pQTL study in 287 normal human liver samples and identified 900 local-pQTL variants and 4,026 distant-pQTL variants. We further discovered 53 genome hotspots of pQTL variants. Transcriptional region mapping analysis showed that 1,133 pQTL variants are in transcriptional regulatory regions. Genomic region enrichment analysis of the identified pQTL variants revealed 804 potential regulatory interactions among 595 regulators (e.g. non-coding RNAs) and 394 proteins. Moreover, pQTL variants and trait-variant integration analysis uncovered several novel mechanisms underlying the relationships between protein expression and liver diseases, such as alcohol dependence. Notably, over 2,000 of the identified pQTL variants have not been reported in previous eQTL studies, suggesting extensive involvement of genetic polymorphisms in post-transcriptional regulation of protein expression in human livers. Conclusions: We have partially established protein expression regulation networks in human livers and generated a wealth of pQTL data that could serve as a valuable resource for the scientific community.
HostingRepository	PRIDE
AnnounceDate	2020-07-21
AnnouncementXML	Submission_2020-09-28_00:30:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bing He
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-13 17:41:17	ID requested
1	2020-07-20 23:13:16	announced
⏵ 2	2020-09-28 00:30:07	announced	2020-09-28: Updated publication reference for PubMed record(s): 32778093.

He B, Shi J, Wang X, Jiang H, Zhu HJ, Genome-wide pQTL analysis of protein expression regulatory networks in the human liver. BMC Biol, 18(1):97(2020) [pubmed]

submitter keyword: DIA,liver,HLS9

Hao-Jie Zhu
contact affiliation	Department of Clinical Pharmacy, University of Michigan
contact email	hjzhu@med.umich.edu
lab head
Bing He
contact affiliation	University of Michigan
contact email	hbing@umich.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/07/PXD019169

PRIDE project URI

• PRIDE
  1. PXD019169
     1. Label: PRIDE project
     2. Name: Genome-wide pQTL analysis of protein expression regulatory networks in the human liver