Evidence map›Paper›PMID 27794045›Full record

ArticleNucleic acids research2017

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A Medvedeva and 15 more

Abstract read
In one paragraph

Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.

0numbers the graph read from it
0cells of the map it votes in
60citing 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

60 citing papers in PubMed.

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  18. Automated methods for cell type annotation on scRNA-seq data.Computational and structural biotechnology journal · 2021
    Review
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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

25 authors.

Marina LizioDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Jayson HarshbargerDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Imad AbugessaisaDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0001-7458-801X
Shuei NoguchiDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Atsushi KondoDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Jessica SeverinDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Chris MungallGenomics Division, Lawrence Berkeley National Laboratory, 84R01, 1 Cyclotron Road, Berkeley, CA 94720, USA.
David ArenillasCentre for Molecular Medicine and Therapeutics at BC Children's Hospital Research, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
Anthony MathelierCentre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.ORCID 0000-0001-5127-5459
Yulia A MedvedevaInstitute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Leninsky prospect, 33, build. 2, 119071 Moscow, Russia.
Andreas LennartssonDepartment of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7-9, 14183 Huddinge, Sweden.
Finn DrabløsDepartment of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), P.O. Box 8905, NO-7491 Trondheim, Norway.
Jordan A RamilowskiDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Owen RackhamProgram in Cardiovascular and Metabolic Disorders, Duke's National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore.
Julian GoughDepartment of Computer Science, University of Bristol, Merchant Venturers Building, Woodland Road, Bristol BS8 1UB UK.
Robin AnderssonThe Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.
Albin SandelinSection for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.
Hans IenasescuSection for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.
Hiromasa OnoDatabase Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima 411-8540, Japan.
Hidemasa BonoDatabase Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima 411-8540, Japan.
Yoshihide HayashizakiPreventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Piero CarninciDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Alistair R R ForrestRIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Takeya KasukawaDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan takeya.kasukawa@riken.jp.
Hideya KawajiDivision of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan kawaji@gsc.riken.jp.

Funding

An Intelligent Concept Agent for Assisting with the Application of MetadataU01HG009453 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI MUNGALL, CHRISTOPHER J · 2016 to 2018
$1.7M
Biotechnology and Biological Sciences Research Council BB/G022771/1NHGRI NIH HHS U01 HG009453
6 · The paper itself

Abstract

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.

Indexed as

Databases, GeneticSoftwareWeb BrowserAnimalsComputational BiologyGene Expression ProfilingGenomicsHumansMammalsSearch Engine

Identifiers

PMID27794045
PMCPMC5210666

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.