ArticleGenome research2020
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Open access · bronzeAbstract read
In one paragraph
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
100citing papers in PubMed, 2 pooled it
–field-weighted citation impact
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.
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.
Who cites it
100 citing papers in PubMed, 2 syntheses or guidelines pooled it, 195 citations in OpenAlex.
- Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set.Life science alliance · 2023Pooled it
- Transcriptional landscape of PTEN loss in primary prostate cancer.BMC cancer · 2021Pooled it
- Confounders of lncRNA screens: sources, consequences and possible solutions.Nature methods · 2026Article
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Deep learning of 777 K bulk transcriptomes reveals human-mouse gene conservation beyond DNA sequence similarity.Communications biology · 2026Article
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- Could Metabolism-Related Long Non-Coding RNAs Be More Conserved than Their Brain-Related Counterparts?Genes · 2026Review
- Multidimensional transcriptome dataset for systematic evaluation of Jakyakgamcho-tang-induced cell signatures.Scientific data · 2026Article
- Identification and histological validation of autophagy-related core genes ADRB2 and PLK2 in keloids, with integrated immune infiltration analysis.Frontiers in immunology · 2026Article
- Functional characterization of DNAAF3-AS1 in chromatin remodeling and H3K36me3 distribution.bioRxiv : the preprint server for biology · 2025Article
- Article
- In vivo detection of antisense HIV-1 transcripts in untreated and ART-treated individuals.Life science alliance · 2025Article
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- Review
- Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.Genome research · 2025Review
- Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing.International journal of molecular sciences · 2025Review
- Cell type-dependent directional transcription at enhancers.NAR genomics and bioinformatics · 2025Article
- A multi-modal transformer for cell type-agnostic regulatory predictions.Cell genomics · 2025Article
- CHASERR-CHD2 dynamics in T cell quiescence and its modulation by cyclosporine.Frontiers in immunology · 2025Article
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
116 authors at 20 institutions in 20 countries.
Jordan A Ramilowski *RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0002-3156-6416
Chi Wai Yip *RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Saumya AgrawalRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Jen-Chien ChangRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Yari CianiLaboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.
Ivan V KulakovskiyEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
Mickaël MendezDepartment of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada.
Jasmine Li Ching OoiRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
John F OuyangProgram in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore.
Nick ParkinsonRoslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom.
Andreas PetriCenter for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark.
Leonie RoosInstitute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.
Jessica SeverinRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Kayoko YasuzawaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Imad AbugessaisaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Altuna AkalinBerlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
Ivan V AntonovInstitute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.
Erik ArnerRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Alessandro BonettiRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Hidemasa BonoGraduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan.ORCID 0000-0003-4413-0651
Beatrice BorsariCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.
Frank BrombacherInternational Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.
Christopher JF CameronSchool of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.
Carlo Vittorio CannistraciBiomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.ORCID 0000-0003-0100-8410
Ryan CardenasInstitute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
Melissa CardonRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Howard ChangCenter for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA.
Josée DostieDepartment of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.
Luca DucoliInstitute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland.
Alexander FavorovDepartment of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
Alexandre FortRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Diego GarridoCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.
Noa GilDepartment of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
Juliette GimenezEpigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy.
Reto GulerInternational Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.
Lusy HandokoRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Jayson HarshbargerRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Akira HasegawaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Yuki HasegawaRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Kosuke HashimotoRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Norihito HayatsuRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Peter HeutinkGenome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany.
Tetsuro HiroseGraduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan.
Eddie L ImadaDepartment of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA.
Masayoshi ItohRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Bogumil KaczkowskiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Aditi KanhereInstitute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
Emily KawabataRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Hideya KawajiRIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan.
Tsugumi KawashimaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
S Thomas KellyRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0003-3904-6690
Miki KojimaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Naoto KondoRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Haruhiko KosekiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Tsukasa KounoRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Anton KratzRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Mariola Kurowska-StolarskaInstitute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom.
Andrew Tae Jun KwonRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Jeffrey LeekDepartment of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA.
Andreas LennartssonDepartment of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.
Marina LizioRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Fernando López-RedondoRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Joachim LuginbühlRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Shiori MaedaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Vsevolod J MakeevDepartment of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
Luigi MarchionniDepartment of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA.
Yulia A MedvedevaInstitute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.
Aki MinodaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Ferenc MüllerInstitute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
Manuel Muñoz-AguirreCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.ORCID 0000-0002-6106-7351
Mitsuyoshi MurataRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Hiromi NishiyoriRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Kazuhiro R NittaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Shuhei NoguchiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Yukihiko NoroRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Ramil NurtdinovCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.
Yasushi OkazakiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Valerio OrlandoBiological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
Denis PaquetteDepartment of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.
Callum J C ParrRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Owen J L RackhamProgram in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore.
Patrizia RizzuGenome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany.
Diego Fernando Sánchez MartinezDepartment of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA.
Albin SandelinDepartment of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark.
Pillay SanjanaInstitute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
Colin A M SempleMRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
Youtaro ShibayamaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Divya M SivaramanRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Takahiro SuzukiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Suzannah C SzumowskiRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Michihira TagamiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Martin S TaylorMRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.ORCID 0000-0001-7656-330X
Chikashi TeraoRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Malte ThodbergDepartment of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark.
Supat ThongjueaRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Vidisha TripathiNational Centre for Cell Science, Pune, Maharashtra 411007, India.
Igor UlitskyDepartment of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
Roberto VerardoLaboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.
Ilya E VorontsovDepartment of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
Chinatsu YamamotoRIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Robert S YoungCentre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom.
J Kenneth BaillieRoslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom.ORCID 0000-0001-5258-793X
Alistair R R ForrestRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.
Michael M HoffmanPrincess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.ORCID 0000-0002-4517-1562
Chung Chau HonRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Takeya KasukawaRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Sakari KauppinenCenter for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark.
Juha KereDepartment of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.
Boris LenhardInstitute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.
Claudio SchneiderLaboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.
Harukazu SuzukiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Ken YagiRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Michiel J L de HoonRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0003-0489-2352
Jay W ShinRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0003-4037-3533
Piero CarninciRIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0001-7202-7243
RIKEN Center for Integrative Medical Sciences · JPJohns Hopkins University · USCentre for Genomic Regulation · ESUniversity of Birmingham · GBAalborg University · DKConsorzio Interuniversitario per le Biotecnologie · ITGerman Center for Neurodegenerative Diseases · DEInstitute of Genetics and Cancer · GBMcGill University · CANational University of Singapore · SGNIHR Imperial Biomedical Research Centre · GBRIKEN · JPRoslin Institute · GBRussian Academy of Sciences · RUSouth African Medical Research Council · ZAUniversity of Copenhagen · DKWeizmann Institute of Science · ILCenter for Systems Biology Dresden · DEÉcole Polytechnique Fédérale de Lausanne · CHEngelhardt Institute of Molecular Biology · RU
Funding
Translational Research Central ServicesP30CA006973 · NCI · JOHNS HOPKINS UNIVERSITY · PI WILLIAM George NELSON · 1985 to 2026
$208.6MHardwiring Mechanism into Predicting Cancer Phenotypes by Computational LearningR01CA200859 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI MARCHIONNI, LUIGI · 2016 to 2020
$1.9MMedical Research Council MC_UP_1102/1Medical Research Council MC_UU_00007/11Medical Research Council MC_UU_00007/16NCI NIH HHS P30 CA006973NCI NIH HHS R01 CA200859
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for
Indexed as
Cell Growth ProcessesCell MovementFibroblastsHumansKCNQ Potassium ChannelsMolecular Sequence AnnotationOligonucleotides, AntisenseRNA, Long NoncodingRNA, Small InterferingKCNQ5 protein, humanKCNQ Potassium ChannelsOligonucleotides, AntisenseRNA, Long NoncodingRNA, Small Interfering
Identifiers
What OpenQuestion holds
Textmetadata
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.