Evidence map›Paper›PMID 25723102›Full record

ArticleGenome biology2015

Gateways to the FANTOM5 promoter level mammalian expression atlas.

Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato and 32 more

Abstract read
In one paragraph

Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 537 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
537citing 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

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

  1. Pooled it
  2. How telomere attrition protects against cancer.Nature reviews. Genetics · 2026
    Review
  3. FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026
    Article
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477 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

42 authors.

Marina Lizio
Jayson Harshbarger
Hisashi Shimoji
Jessica Severin
Takeya Kasukawa
Serkan Sahin
Imad Abugessaisa
Shiro Fukuda
Fumi Hori
Sachi Ishikawa-Kato
Christopher J Mungall
Erik Arner
J Kenneth Baillie
Nicolas Bertin
Hidemasa Bono
Michiel de Hoon
Alexander D Diehl
Emmanuel Dimont
Tom C Freeman
Kaori Fujieda
Winston Hide
Rajaram Kaliyaperumal
Toshiaki Katayama
Timo Lassmann
Terrence F Meehan
Koro Nishikata
Hiromasa Ono
Michael Rehli
Albin Sandelin
Erik A Schultes
Peter A C 't Hoen
Zuotian Tatum
Mark Thompson
Tetsuro Toyoda
Derek W Wright
Carsten O Daub
Masayoshi Itoh
Piero Carninci
Yoshihide Hayashizaki
Alistair R R Forrest
Hideya Kawaji
FANTOM consortium

Funding

The Monarch Initiative: Linking Diseases to Model Organism ResourcesR24OD011883 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAENDEL, MELISSA A, MUNGALL, CHRISTOPHER J · 2012 to 2024
$16.0M
Biotechnology and Biological Sciences Research Council BB/F003722/1Biotechnology and Biological Sciences Research Council BB/I001107/1Biotechnology and Biological Sciences Research Council BB/JO1446X/1NIH HHS R24 OD011883
6 · The paper itself

Abstract

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.

Indexed as

Promoter Regions, GeneticSoftwareTranscription Initiation, GeneticAnimalsComputational BiologyDatabases, GeneticDatasets as TopicGene Expression ProfilingGenomicsHumansMiceTranscriptomeUser-Computer Interface

Identifiers

PMID25723102
PMCPMC4310165

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.