Collection

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.

Read the Comment from the FANTOM5 organizers announcing the launch of this collection

Data Descriptors

  • Scientific Data | Data Descriptor | open

    • Shuhei Noguchi
    • , Takahiro Arakawa
    • , Shiro Fukuda
    • , Masaaki Furuno
    • , Akira Hasegawa
    • , Fumi Hori
    • , Sachi Ishikawa-Kato
    • , Kaoru Kaida
    • , Ai Kaiho
    • , Mutsumi Kanamori-Katayama
    • , Tsugumi Kawashima
    • , Miki Kojima
    • , Atsutaka Kubosaki
    • , Ri-ichiroh Manabe
    • , Mitsuyoshi Murata
    • , Sayaka Nagao-Sato
    • , Kenichi Nakazato
    • , Noriko Ninomiya
    • , Hiromi Nishiyori-Sueki
    • , Shohei Noma
    • , Eri Saijyo
    • , Akiko Saka
    • , Mizuho Sakai
    • , Christophe Simon
    • , Naoko Suzuki
    • , Michihira Tagami
    • , Shoko Watanabe
    • , Shigehiro Yoshida
    • , Peter Arner
    • , Richard A. Axton
    • , Magda Babina
    • , J. Kenneth Baillie
    • , Timothy C. Barnett
    • , Anthony G. Beckhouse
    • , Antje Blumenthal
    • , Beatrice Bodega
    • , Alessandro Bonetti
    • , James Briggs
    • , Frank Brombacher
    • , Ailsa J. Carlisle
    • , Hans C. Clevers
    • , Carrie A. Davis
    • , Michael Detmar
    • , Taeko Dohi
    • , Albert S.B. Edge
    • , Matthias Edinger
    • , Anna Ehrlund
    • , Karl Ekwall
    • , Mitsuhiro Endoh
    • , Hideki Enomoto
    • , Afsaneh Eslami
    • , Michela Fagiolini
    • , Lynsey Fairbairn
    • , Mary C. Farach-Carson
    • , Geoffrey J. Faulkner
    • , Carmelo Ferrai
    • , Malcolm E. Fisher
    • , Lesley M. Forrester
    • , Rie Fujita
    • , Jun-ichi Furusawa
    • , Teunis B. Geijtenbeek
    • , Thomas Gingeras
    • , Daniel Goldowitz
    • , Sven Guhl
    • , Reto Guler
    • , Stefano Gustincich
    • , Thomas J. Ha
    • , Masahide Hamaguchi
    • , Mitsuko Hara
    • , Yuki Hasegawa
    • , Meenhard Herlyn
    • , Peter Heutink
    • , Kelly J. Hitchens
    • , David A. Hume
    • , Tomokatsu Ikawa
    • , Yuri Ishizu
    • , Chieko Kai
    • , Hiroshi Kawamoto
    • , Yuki I. Kawamura
    • , Judith S. Kempfle
    • , Tony J. Kenna
    • , Juha Kere
    • , Levon M. Khachigian
    • , Toshio Kitamura
    • , Sarah Klein
    • , S. Peter Klinken
    • , Alan J. Knox
    • , Soichi Kojima
    • , Haruhiko Koseki
    • , Shigeo Koyasu
    • , Weonju Lee
    • , Andreas Lennartsson
    • , Alan Mackay-sim
    • , Niklas Mejhert
    • , Yosuke Mizuno
    • , Hiromasa Morikawa
    • , Mitsuru Morimoto
    • , Kazuyo Moro
    • , Kelly J. Morris
    • , Hozumi Motohashi
    • , Christine L. Mummery
    • , Yutaka Nakachi
    • , Fumio Nakahara
    • , Toshiyuki Nakamura
    • , Yukio Nakamura
    • , Tadasuke Nozaki
    • , Soichi Ogishima
    • , Naganari Ohkura
    • , Hiroshi Ohno
    • , Mitsuhiro Ohshima
    • , Mariko Okada-Hatakeyama
    • , Yasushi Okazaki
    • , Valerio Orlando
    • , Dmitry A. Ovchinnikov
    • , Robert Passier
    • , Margaret Patrikakis
    • , Ana Pombo
    • , Swati Pradhan-Bhatt
    • , Xian-Yang Qin
    • , Michael Rehli
    • , Patrizia Rizzu
    • , Sugata Roy
    • , Antti Sajantila
    • , Shimon Sakaguchi
    • , Hiroki Sato
    • , Hironori Satoh
    • , Suzana Savvi
    • , Alka Saxena
    • , Christian Schmidl
    • , Claudio Schneider
    • , Gundula G. Schulze-Tanzil
    • , Anita Schwegmann
    • , Guojun Sheng
    • , Jay W. Shin
    • , Daisuke Sugiyama
    • , Takaaki Sugiyama
    • , Kim M. Summers
    • , Naoko Takahashi
    • , Jun Takai
    • , Hiroshi Tanaka
    • , Hideki Tatsukawa
    • , Andru Tomoiu
    • , Hiroo Toyoda
    • , Marc van de Wetering
    • , Linda M. van den Berg
    • , Roberto Verardo
    • , Dipti Vijayan
    • , Christine A. Wells
    • , Louise N. Winteringham
    • , Ernst Wolvetang
    • , Yoko Yamaguchi
    • , Masayuki Yamamoto
    • , Chiyo Yanagi-Mizuochi
    • , Misako Yoneda
    • , Yohei Yonekura
    • , Peter G. Zhang
    • , Silvia Zucchelli
    • , Imad Abugessaisa
    • , Erik Arner
    • , Jayson Harshbarger
    • , Atsushi Kondo
    • , Timo Lassmann
    • , Marina Lizio
    • , Serkan Sahin
    • , Thierry Sengstag
    • , Jessica Severin
    • , Hisashi Shimoji
    • , Masanori Suzuki
    • , Harukazu Suzuki
    • , Jun Kawai
    • , Naoto Kondo
    • , Masayoshi Itoh
    • , Carsten O. Daub
    • , Takeya Kasukawa
    • , Hideya Kawaji
    • , Piero Carninci
    • , Alistair R.R. Forrest
    •  &  Yoshihide Hayashizaki

Research & Analysis

  • Nature Biotechnology | Resource

    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
  • Nature | Article

    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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