Evidence map›Paper›PMID 34863093›Full record

ArticleBMC genomics2021

Genetic architecture of protein expression and its regulation in the mouse brain.

Alyssa Erickson, Suiping Zhou, Jie Luo, Ling Li, Xin Huang, Zachary Even, He Huang, Hai-Ming Xu, Junmin Peng, Lu Lu and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.7field-weighted citation impact, top 33% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 7 citations in OpenAlex.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 5 institutions in 2 countries.

Alyssa EricksonDepartment of Biology, University of North Dakota, Grand Forks, ND, 58202, USA.
Suiping ZhouCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38163, USA.
Jie LuoCentral Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Ling LiDepartment of Biology, University of North Dakota, Grand Forks, ND, 58202, USA.
Xin HuangInstitute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
Zachary EvenDepartment of Biology, University of North Dakota, Grand Forks, ND, 58202, USA.
He HuangDepartment of Biology, University of North Dakota, Grand Forks, ND, 58202, USA.
Hai-Ming XuInstitute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
Junmin PengCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38163, USA.
Lu LuDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
Xusheng WangDepartment of Biology, University of North Dakota, Grand Forks, ND, 58202, USA. xusheng.wang@und.edu.ORCID http://orcid.org/0000-0002-1759-9588
University of North Dakota · USSt. Jude Children's Research Hospital · USZhejiang University · CNUniversity of Tennessee Health Science Center · USZheJiang Academy of Agricultural Sciences · CN

Funding

The role of class IIa Hdac in regulating cell fate choice in early cortical development.P20GM104360 · NIGMS · UNIVERSITY OF NORTH DAKOTA · PI VAUGHAN, ROXANNE A · 2013 to 2023
$21.1M
Tracking and Evaluation CoreU54GM128729 · NIGMS · UNIVERSITY OF NORTH DAKOTA · PI BASSON, MARC D. · 2018 to 2022
$20.3M
NIGMS NIH HHS P20 GM104360NIGMS NIH HHS U54 GM128729NIH HHS 5P20GM104360-07
6 · The paper itself

Abstract

backgroundNatural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6 J (B6) and DBA/2 J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology.

resultsBy comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and characterized the genetic basis of protein expression. We further applied a proteogenomic approach to detect variant peptides and define protein allele-specific expression (pASE), identifying 33 variant peptides with cis-effects and 17 variant peptides showing trans-effects. Comparison of regulation at transcript and protein levels show a significant divergence.

conclusionsThe results provide a comprehensive analysis of genetic architecture of protein expression and the contribution of cis- and trans-acting regulatory differences to protein expression.

Indexed as

BrainTandem Mass SpectrometryAnimalsChromatography, LiquidMiceMice, Inbred C57BLMice, Inbred DBAAllele-specific expressionBrainMass spectrometryMouseProtein expressionProtein regulationProteome

Identifiers

PMID34863093
PMCPMC8642946
OpenAlexW4225655888

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.