Scientific Data | Data Descriptor | open
The FANTOM5 project
FANTOM (Functional ANnoTation Of the Mammalian genome) is an international research consortium led by RIKEN focused on functional annotation of mammalian genomes and characterization of transcriptional regulatory networks. In FANTOM5 the consortium, consisting of over 500 international members from 20 countries, has generated maps of human regulatory elements and transcriptional regulatory network models. To achieve this they use CAGE (Cap Analysis of Gene Expression) sequencing on RNA samples from every major human organ, multiple primary cell types, over 200 cancer cell lines, 30 time courses of cellular differentiation, and mouse developmental time courses.
This collection brings together research articles, analyses, resource papers and letters from FANTOM5, as well as descriptions of the data generated by the project, all of which have been published by Nature Research.
FANTOM5 organizers published a Comment announcing the launch of this collection and have been interviewed on their contributions to FANTOM5.
Data Descriptors
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Scientific Data | Data Descriptor | open
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
- Margherita Francescatto
- , Marina Lizio
- , Ingrid Philippens
- , Luba M. Pardo
- , Ronald Bontrop
- , Mizuho Sakai
- , Shoko Watanabe
- , Masayoshi Itoh
- , Akira Hasegawa
- , Timo Lassmann
- , Jessica Severin
- , Jayson Harshbarger
- , Imad Abugessaisa
- , Takeya Kasukawa
- , Piero Carninci
- , Yoshihide Hayashizaki
- , Alistair R. R. Forrest
- , Hideya Kawaji
- , Patrizia Rizzu
- & Peter Heutink
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Scientific Data | Data Descriptor | open
Linking FANTOM5 CAGE peaks to annotations with CAGEscan
- Nicolas Bertin
- , Mickaël Mendez
- , Akira Hasegawa
- , Marina Lizio
- , Imad Abugessaisa
- , Jessica Severin
- , Mizuho Sakai-Ohno
- , Timo Lassmann
- , Takeya Kasukawa
- , Hideya Kawaji
- , Yoshihide Hayashizaki
- , Alistair R. R. Forrest
- , Piero Carninci
- & Charles Plessy
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Scientific Data | Data Descriptor | open
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
- Imad Abugessaisa
- , Shuhei Noguchi
- , Akira Hasegawa
- , Jayson Harshbarger
- , Atsushi Kondo
- , Marina Lizio
- , Jessica Severin
- , Piero Carninci
- , Hideya Kawaji
- & Takeya Kasukawa
Research & Analysis
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Scientific Data | Analysis | open
Distinct transcriptional responses of lymphatic endothelial cells to VEGFR-3 and VEGFR-2 stimulation
- Lothar C. Dieterich
- , Luca Ducoli
- , Jay W. Shin
- & Michael Detmar
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Scientific Data | Article | open
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes
- Hiromasa Ono
- , Osamu Ogasawara
- , Kosaku Okubo
- & Hidemasa Bono
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Nature Biotechnology | Resource
An integrated expression atlas of miRNAs and their promoters in human and mouse
An atlas of microRNA expression patterns and regulators is produced by deep sequencing of short RNAs in human and mouse cells.
- Derek de Rie
- , Imad Abugessaisa
- , Tanvir Alam
- , Erik Arner
- , Peter Arner
- , Haitham Ashoor
- , Gaby Åström
- , Magda Babina
- , Nicolas Bertin
- , A Maxwell Burroughs
- , Ailsa J Carlisle
- , Carsten O Daub
- , Michael Detmar
- , Ruslan Deviatiiarov
- , Alexandre Fort
- , Claudia Gebhard
- , Daniel Goldowitz
- , Sven Guhl
- , Thomas J Ha
- , Jayson Harshbarger
- , Akira Hasegawa
- , Kosuke Hashimoto
- , Meenhard Herlyn
- , Peter Heutink
- , Kelly J Hitchens
- , Chung Chau Hon
- , Edward Huang
- , Yuri Ishizu
- , Chieko Kai
- , Takeya Kasukawa
- , Peter Klinken
- , Timo Lassmann
- , Charles-Henri Lecellier
- , Weonju Lee
- , Marina Lizio
- , Vsevolod Makeev
- , Anthony Mathelier
- , Yulia A Medvedeva
- , Niklas Mejhert
- , Christopher J Mungall
- , Shohei Noma
- , Mitsuhiro Ohshima
- , Mariko Okada-Hatakeyama
- , Helena Persson
- , Patrizia Rizzu
- , Filip Roudnicky
- , Pål Sætrom
- , Hiroki Sato
- , Jessica Severin
- , Jay W Shin
- , Rolf K Swoboda
- , Hiroshi Tarui
- , Hiroo Toyoda
- , Kristoffer Vitting-Seerup
- , Louise Winteringham
- , Yoko Yamaguchi
- , Kayoko Yasuzawa
- , Misako Yoneda
- , Noriko Yumoto
- , Susan Zabierowski
- , Peter G Zhang
- , Christine A Wells
- , Kim M Summers
- , Hideya Kawaji
- , Albin Sandelin
- , Michael Rehli
- , The FANTOM Consortium
- , Yoshihide Hayashizaki
- , Piero Carninci
- , Alistair R R Forrest
- & Michiel J L de Hoon
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Nature | Article
An atlas of human long non-coding RNAs with accurate 5′ ends
A catalogue of human long non-coding RNA genes and their expression profiles across samples from major human primary cell types, tissues and cell lines.
- Chung-Chau Hon
- , Jordan A. Ramilowski
- , Jayson Harshbarger
- , Nicolas Bertin
- , Owen J. L. Rackham
- , Julian Gough
- , Elena Denisenko
- , Sebastian Schmeier
- , Thomas M. Poulsen
- , Jessica Severin
- , Marina Lizio
- , Hideya Kawaji
- , Takeya Kasukawa
- , Masayoshi Itoh
- , A. Maxwell Burroughs
- , Shohei Noma
- , Sarah Djebali
- , Tanvir Alam
- , Yulia A. Medvedeva
- , Alison C. Testa
- , Leonard Lipovich
- , Chi-Wai Yip
- , Imad Abugessaisa
- , Mickaël Mendez
- , Akira Hasegawa
- , Dave Tang
- , Timo Lassmann
- , Peter Heutink
- , Magda Babina
- , Christine A. Wells
- , Soichi Kojima
- , Yukio Nakamura
- , Harukazu Suzuki
- , Carsten O. Daub
- , Michiel J. L. de Hoon
- , Erik Arner
- , Yoshihide Hayashizaki
- , Piero Carninci
- & Alistair R. R. Forrest
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Scientific Reports | Article | open
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses
- Chih-yu Chen
- , Wenqiang Shi
- , Bradley P. Balaton
- , Allison M. Matthews
- , Yifeng Li
- , David J. Arenillas
- , Anthony Mathelier
- , Masayoshi Itoh
- , Hideya Kawaji
- , Timo Lassmann
- , Yoshihide Hayashizaki
- , Piero Carninci
- , Alistair R. R. Forrest
- , Carolyn J. Brown
- & Wyeth W. Wasserman
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Scientific Reports | Article | open
Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis
- Masafumi Horie
- , Yoko Yamaguchi
- , Akira Saito
- , Takahide Nagase
- , Marina Lizio
- , Masayoshi Itoh
- , Hideya Kawaji
- , Timo Lassmann
- , Piero Carninci
- , Alistair R. R. Forrest
- , Yoshihide Hayashizaki
- , Tatsuo Suzutani
- , Kai Kappert
- , Patrick Micke
- & Mitsuhiro Ohshima
News & Comments
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Scientific Data | Comment | open
The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types
- Hideya Kawaji
- , Takeya Kasukawa
- , Alistair Forrest
- , Piero Carninci
- & Yoshihide Hayashizaki
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Nature Biotechnology | Correspondence
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU
- Jessica Severin
- , Marina Lizio
- , Jayson Harshbarger
- , Hideya Kawaji
- , Carsten O Daub
- , Yoshihide Hayashizaki
- , The FANTOM Consortium
- , Nicolas Bertin
- & Alistair R R Forrest