Evidence map›Paper›PMID 25848752›Full record

ArticleNature genetics2015

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse.

Tomas Babak, Brian DeVeale, Emily K Tsang, Yiqi Zhou, Xin Li, Kevin S Smith, Kim R Kukurba, Rui Zhang, Jin Billy Li, Derek van der Kooy and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
137citing papers in PubMed, 2 pooled it
–field-weighted citation impact
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

137 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Article
  17. Review
  18. Article
  19. Article
  20. Article

77 more citing papers are in PubMed but not listed here.

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

12 authors.

Tomas BabakDepartment of Biology, Stanford University, Stanford, California, USA.
Brian DeVealeUniversity of California San Francisco School of Medicine, University of California, San Francisco, San Francisco, California, USA.
Emily K TsangDepartment of Pathology, Stanford University, Stanford, California, USA.
Yiqi ZhouDepartment of Biology, Stanford University, Stanford, California, USA.
Xin LiDepartment of Pathology, Stanford University, Stanford, California, USA.
Kevin S SmithDepartment of Pathology, Stanford University, Stanford, California, USA.
Kim R Kukurba1] Department of Pathology, Stanford University, Stanford, California, USA. [2] Department of Genetics, Stanford University, Stanford, California, USA.
Rui ZhangDepartment of Genetics, Stanford University, Stanford, California, USA.
Jin Billy LiDepartment of Genetics, Stanford University, Stanford, California, USA.ORCID 0000000307131399
Derek van der KooyDepartment of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Stephen B Montgomery1] Department of Pathology, Stanford University, Stanford, California, USA. [2] Department of Genetics, Stanford University, Stanford, California, USA.
Hunter B FraserDepartment of Biology, Stanford University, Stanford, California, USA.

Funding

Yeast as a model for understanding gene expression adaptationR01GM097171 · NIGMS · STANFORD UNIVERSITY · PI FRASER, HUNTER B · 2012 to 2024
$4.2M
LIMBIC &MEDULLARY MECH. IN COCAINE-RELATED SUDDEN DEATHR01DA006227 · NIDA · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI MASH, DEBORAH C. · 1990 to 2012
$3.7M
HIGH RESOLUTION ALLELE SPECIFIC EXPRESSION ASSAYSU01HG007593 · NHGRI · STANFORD UNIVERSITY · PI LI, JIN BILLY · 2014 to 2016
$1.3M
Statistical analysis of gene expression quantitative trait loci (eQTL)R01MH090951 · NIMH · UNIVERSITY OF CHICAGO · PI PRITCHARD, JONATHAN K · 2010 to 2012
$873k
Methods for high-resolution analysis of genetic effects on gene expressionR01MH090941 · NIMH · UNIVERSITY OF GENEVA · PI DERMITZAKIS, EMMANOUIL, GUIGO, RODERIC · 2010 to 2012
$863k
FACILITATING GTEx, DISEASE, AND GxE ANALYSES VIA FAST EXPRESSION (e)QTL MAPPINGR01MH090936 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI NOBEL, ANDREW B, RUSYN, IVAN · 2010 to 2012
$847k
Using the Transcriptome for SNP and Gene AnnotationR01MH090937 · NIMH · UNIVERSITY OF CHICAGO · PI COX, NANCY J, NICOLAE, DAN LIVIU · 2010 to 2012
$825k
Epistatic and Cross Tissue Analysis for Human Gene Expression TraitsR01MH090948 · NIMH · HARVARD UNIVERSITY · PI LIU, JUN S · 2010 to 2011
$588k
CCR NIH HHS HHSN261200800001CNCI NIH HHS HHSN261200800001ENHGRI NIH HHS U01 HG007593NHGRI NIH HHS U01HG007593NHLBI NIH HHS HHSN268201000029CNIDA NIH HHS R01 DA006227NIGMS NIH HHS 1R01GM097171-01A1NIGMS NIH HHS R01 GM097171NIMH NIH HHS MH090936NIMH NIH HHS MH090937NIMH NIH HHS MH090941NIMH NIH HHS MH090948NIMH NIH HHS MH090951NIMH NIH HHS R01 MH090936NIMH NIH HHS R01 MH090937NIMH NIH HHS R01 MH090941NIMH NIH HHS R01 MH090948NIMH NIH HHS R01 MH090951
6 · The paper itself

Abstract

Genomic imprinting is an epigenetic process that restricts gene expression to either the maternally or paternally inherited allele. Many theories have been proposed to explain its evolutionary origin, but understanding has been limited by a paucity of data mapping the breadth and dynamics of imprinting within any organism. We generated an atlas of imprinting spanning 33 mouse and 45 human developmental stages and tissues. Nearly all imprinted genes were imprinted in early development and either retained their parent-of-origin expression in adults or lost it completely. Consistent with an evolutionary signature of parental conflict, imprinted genes were enriched for coexpressed pairs of maternally and paternally expressed genes, showed accelerated expression divergence between human and mouse, and were more highly expressed than their non-imprinted orthologs in other species. Our approach demonstrates a general framework for the discovery of imprinting in any species and sheds light on the causes and consequences of genomic imprinting in mammals.

Indexed as

Genomic ImprintingAnimalsGene ExpressionGenome, HumanHumansMiceMice, Inbred C57BLOrgan SpecificityPolymorphism, Single Nucleotide

Identifiers

PMID25848752
PMCPMC4414907

What OpenQuestion holds

Textmetadata
LicenceTDM
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.