Evidence map›Paper›PMID 24510058›Full record

ArticleNature communications2014

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

Ying Yu, James C Fuscoe, Chen Zhao, Chao Guo, Meiwen Jia, Tao Qing, Desmond I Bannon, Lee Lancashire, Wenjun Bao, Tingting Du and 23 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 229 papers.

0numbers the graph read from it
0cells of the map it votes in
229citing papers in PubMed
–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

229 citing papers in PubMed.

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  8. Gene function predicts divergence across molecular levels.bioRxiv : the preprint server for biology · 2026
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  16. Article
  17. TIPE2: a novel regulatory factor for cardiovascular-related diseases.Journal of molecular medicine (Berlin, Germany) · 2025
    Review
  18. TheBiomolecules · 2025
    Review
  19. Article
  20. Article

169 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

33 authors.

Ying Yu1] Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China [2].
James C Fuscoe1] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [2].
Chen ZhaoCenter for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China.
Chao GuoFunctional Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA.
Meiwen JiaCenter for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China.
Tao QingCenter for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China.
Desmond I BannonArmy Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground, Maryland 21010, USA.
Lee LancashireComputation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
Wenjun BaoSAS Institute Inc., Cary, North Carolina 27513, USA.
Tingting DuCenter for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China.
Heng LuoCenter for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China.
Zhenqiang SuNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Wendell D JonesExpression Analysis Inc., Durham, North Carolina 27713, USA.
Carrie L MolandNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
William S BranhamNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Feng QianNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Baitang NingNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Yan LiNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Huixiao HongNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Lei GuoNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Nan MeiNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Tieliu ShiThe Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science, Shanghai 200241, China.
Kevin Y WangJohns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Russell D WolfingerSAS Institute Inc., Cary, North Carolina 27513, USA.
Yuri NikolskyComputation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
Stephen J WalkerWake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, USA.
Penelope Duerksen-HughesDepartment of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
Christopher E MasonDepartment of Physiology & Biophysics and the Institute for Computational Biomedicine, Cornell University, New York, New York 10021, USA.
Weida TongNational Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
Jean Thierry-MiegNational Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
Danielle Thierry-MiegNational Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
Leming Shi1] Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China [2] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [3] Fudan-Zhangjiang Center for Clinical Genomics and Zhangjiang Center for Translational Medicine, Shanghai 201203, China.
Charles WangCenter for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.

Funding

Intramural NIH HHS
6 · The paper itself

Abstract

The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model.

Indexed as

TranscriptomeAlternative SplicingAnimalsFemaleGene Expression ProfilingMaleProtein IsoformsRats, Inbred F344Sequence Analysis, RNASex CharacteristicsProtein Isoforms

Identifiers

PMID24510058
PMCPMC3926002

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.