Evidence map›Paper›PMID 25599403›Full record

SynthesisNature genetics2015

The landscape of long noncoding RNAs in the human transcriptome.

Matthew K Iyer, Yashar S Niknafs, Rohit Malik, Udit Singhal, Anirban Sahu, Yasuyuki Hosono, Terrence R Barrette, John R Prensner, Joseph R Evans, Shuang Zhao and 9 more

Abstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,638 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,638citing papers in PubMed, 1 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

1,638 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Review
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  7. Article
  8. RNA regulation in plants.Science China. Life sciences · 2026
    Review
  9. Article
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  14. Article
  15. The hidden players: LncRNA-Encoded micropeptides in cancer hallmarks.Cellular and molecular life sciences : CMLS · 2026
    Review
  16. Article
  17. Article
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  19. Integrative transcriptomic analysis reveals alternative splicing programs in sepsis-induced myocardial injury across dual mouse models.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026
    Article
  20. Review

1,578 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

19 authors.

Matthew K Iyer1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan, USA.
Yashar S Niknafs1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.
Rohit Malik1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Udit Singhal1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA.
Anirban Sahu1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Yasuyuki HosonoMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Terrence R BarretteMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
John R PrensnerMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Joseph R Evans1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA.
Shuang Zhao1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA.
Anton PoliakovMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Xuhong Cao1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA.
Saravana M Dhanasekaran1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Yi-Mi WuMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Dan R RobinsonMichigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
David G Beer1] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA. [2] Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA.
Felix Y Feng1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA. [3] Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA.
Hariharan K IyerDepartment of Statistics, Colorado State University, Fort Collins, Colorado, USA.
Arul M Chinnaiyan1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan, USA. [3] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [4] Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA. [5] Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA. [6] Department of Urology, University of Michigan, Ann Arbor, Michigan, USA.

Funding

MICHIGAN MEDICAL SCIENTIST TRAINING PROGRAMT32GM007863 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI COLLINS, KATHLEEN L. · 1985 to 2024
$38.3M
VACCINIA PSA FOR ANDROGEN-MODULATED POST-SURGICAL RECURRENCE OF PROSTATE CANCERP50CA069568 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI COONEY, KATHLEEN A · 1995 to 2013
$31.3M
Tissue/InformaticsP50CA186786 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Robert Timothy Dess · 2014 to 2026
$27.6M
CELLULAR AND MOLECULAR BIOLOGY AT MICHIGANT32GM007315 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI PUTHENVEEDU, MANOJKUMAR A · 1985 to 2021
$12.8M
Epitomic Biomarkers of Prostate CancerU01CA111275 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M, RUBIN, MARK A. · 2004 to 2015
$6.8M
Identification and Characterization of Gene Fusions in Lung AdenocarcinomaR01CA154365 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BEER, DAVID GEORGE, CHINNAIYAN, ARUL M · 2011 to 2015
$1.4M
Molecuar Sub-typing of Prostate Cancer Based on Recurrent Gene FusionsR01CA132874 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M · 2009 to 2013
$1.2M
The role of long non-coding RNA SChLAP-1 in prostate cancerF30CA180376 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI SAHU, ANIRBAN · 2013 to 2015
$114k
Howard Hughes Medical InstituteNCI NIH HHS F30 CA180376NCI NIH HHS P50 CA069568NCI NIH HHS P50 CA186786NCI NIH HHS P50 CA69568NCI NIH HHS R01 CA132874NCI NIH HHS R01 CA154365NCI NIH HHS U01 CA111275NIGMS NIH HHS T32 GM007315NIGMS NIH HHS T32 GM007863
6 · The paper itself

Abstract

Long noncoding RNAs (lncRNAs) are emerging as important regulators of tissue physiology and disease processes including cancer. To delineate genome-wide lncRNA expression, we curated 7,256 RNA sequencing (RNA-seq) libraries from tumors, normal tissues and cell lines comprising over 43 Tb of sequence from 25 independent studies. We applied ab initio assembly methodology to this data set, yielding a consensus human transcriptome of 91,013 expressed genes. Over 68% (58,648) of genes were classified as lncRNAs, of which 79% were previously unannotated. About 1% (597) of the lncRNAs harbored ultraconserved elements, and 7% (3,900) overlapped disease-associated SNPs. To prioritize lineage-specific, disease-associated lncRNA expression, we employed non-parametric differential expression testing and nominated 7,942 lineage- or cancer-associated lncRNA genes. The lncRNA landscape characterized here may shed light on normal biology and cancer pathogenesis and may be valuable for future biomarker development.

Indexed as

TranscriptomeCell LineCell Line, TumorGene ExpressionHumansNeoplasmsRNA, Long NoncodingSequence Analysis, RNARNA, Long Noncoding

Identifiers

PMID25599403
PMCPMC4417758

What OpenQuestion holds

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Read underepoch 390

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.