Evidence map›Paper›PMID 25953952›Full record

ArticleGenome research2015

The landscape of genomic imprinting across diverse adult human tissues.

Yael Baran, Meena Subramaniam, Anne Biton, Taru Tukiainen, Emily K Tsang, Manuel A Rivas, Matti Pirinen, Maria Gutierrez-Arcelus, Kevin S Smith, Kim R Kukurba and 13 more

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

Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
140citing 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

140 citing papers in PubMed, 2 syntheses or guidelines pooled it, 237 citations in OpenAlex.

  1. Pooled it
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  13. Epigenetics · 2025
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80 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

23 authors at 10 institutions in 6 countries.

Yael BaranThe Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel;
Meena SubramaniamDepartment of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
Anne BitonDepartment of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
Taru TukiainenAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
Emily K TsangDepartment of Pathology, Stanford University, Stanford, California 94305, USA; Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA;
Manuel A RivasWellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom;
Matti PirinenInstitute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland;
Maria Gutierrez-ArcelusDepartment of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland;
Kevin S SmithDepartment of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
Kim R KukurbaDepartment of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
Rui ZhangDepartment of Genetics, Stanford University, Stanford, California 94305, USA;
Celeste EngDepartment of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
Dara G TorgersonDepartment of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
Cydney UrbanekIntegrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA;
GTEx Consortium
Jin Billy LiDepartment of Genetics, Stanford University, Stanford, California 94305, USA;
Jose R Rodriguez-SantanaCentro de Neumología Pediátrica, San Juan, Puerto Rico, 00917;
Esteban G BurchardDepartment of Medicine, University of California San Francisco, San Francisco, California 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA;
Max A SeiboldIntegrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA; Department of Pediatrics, National Jewish Health, Denver, Colorado 80206, USA; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Denver, Denver, Colorado 80045, USA;
Daniel G MacArthurAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
Stephen B MontgomeryDepartment of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
Noah A ZaitlenDepartment of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
Tuuli LappalainenNew York Genome Center, New York, New York 10013, USA; Department of Systems Biology, Columbia University, New York, New York 10032, USA.
Stanford University · USUniversity of California, San Francisco · USBroad Institute · USNational Jewish Health · USCentre for Human Genetics · GBCentro de Neumologia Pediatrica · PRNew York Genome Center · USTel Aviv University · ILUniversity of Geneva · CHUniversity of Helsinki · FI

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
BMI Bioinformatics Training GrantsT32GM067547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HERNANDEZ, RYAN D. · 2003 to 2022
$6.6M
LIMBIC &MEDULLARY MECH. IN COCAINE-RELATED SUDDEN DEATHR01DA006227 · NIDA · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI MASH, DEBORAH C. · 1990 to 2012
$3.7M
Integrative Program in Complex Biological System (ipCBS)T32EB009383 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MARSHALL, WALLACE, WEINER, ORION D · 2009 to 2022
$3.2M
Methods for high-resolution analysis of genetic effects on gene expressionR01MH101814 · NIMH · UNIVERSITY OF GENEVA · PI BUSTAMANTE, CARLOS DANIEL, DERMITZAKIS, EMMANOUIL · 2013 to 2016
$2.3M
Massively parallel identification of functional 3' UTR variants in asthmaR01HL124285 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ERLE, DAVID J · 2014 to 2017
$2.2M
Empiric deconvolution of functional RNA elementsR01GM110251 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ERLE, DAVID J, MCMANUS, MICHAEL T · 2014 to 2017
$2.2M
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
Richer Models of Asthma Risk: Bridging the Environment-Genetics DivideK25HL121295 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ZAITLEN, NOAH A · 2014 to 2018
$784k
CCR NIH HHS HHSN261200800001CNCI NIH HHS HHSN261200800001ENHGRI NIH HHS U54 HG003067NHLBI NIH HHS 1K25HL121295-01A1NHLBI NIH HHS 1R01HL124285-01NHLBI NIH HHS HHSN268201000029CNHLBI NIH HHS K25 HL121295NHLBI NIH HHS R01 HL124285NIBIB NIH HHS T32 EB009383NIDA NIH HHS DA006227NIDA NIH HHS R01 DA006227NIGMS NIH HHS 1R01GM110251-01NIGMS NIH HHS R01 GM110251NIGMS NIH HHS T32 GM067547NIMH NIH HHS MH090936NIMH NIH HHS MH090937NIMH 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 MH090951NIMH NIH HHS R01 MH101814NIMH NIH HHS R01MH101814PHS HHS HHSN26820100029C
6 · The paper itself

Abstract

Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues.

Indexed as

Genomic ImprintingGenomicsAdultAllelesCluster AnalysisDatabases, Nucleic AcidDNA MethylationFemaleGene Expression RegulationGenetic VariationGenotypeHumansMaleOrgan SpecificityPolymorphism, Single NucleotideReproducibility of Results

Identifiers

PMID25953952
PMCPMC4484390
OpenAlexW2144824933

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

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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.