Collection

The FANTOM5 project

  • 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
  • Nature Genetics | Letter

    Owen Rackham, Jose Polo, Julian Gough and colleagues present a method, Mogrify, for predicting sets of transcription factors that can induce transdifferentiation between cell types. They show that Mogrify is able to predict known factors for published cell conversions and experimentally validate factors for two new conversions.

    • Owen J L Rackham
    • , Jaber Firas
    • , Hai Fang
    • , Matt E Oates
    • , Melissa L Holmes
    • , Anja S Knaupp
    • , The FANTOM Consortium
    • , Harukazu Suzuki
    • , Christian M Nefzger
    • , Carsten O Daub
    • , Jay W Shin
    • , Enrico Petretto
    • , Alistair R R Forrest
    • , Yoshihide Hayashizaki
    • , Jose M Polo
    •  &  Julian Gough
  • Nature Genetics | Analysis

    Hilary Finucane, Brendan Bulik-Sullivan, Benjamin Neale, Alkes Price and colleagues introduce a new method, called stratified LD score regression, for partitioning heritability by functional category using genome-wide association study summary statistics. They observe a substantial enrichment of heritability in conserved regions and illustrate how this approach can provide insights into the biological basis of disease and direction for functional follow-up.

    • Hilary K Finucane
    • , Brendan Bulik-Sullivan
    • , Alexander Gusev
    • , Gosia Trynka
    • , Yakir Reshef
    • , Po-Ru Loh
    • , Verneri Anttila
    • , Han Xu
    • , Chongzhi Zang
    • , Kyle Farh
    • , Stephan Ripke
    • , Felix R Day
    • , ReproGen Consortium
    • , Schizophrenia Working Group of the Psychiatric Genomics Consortium
    • , The RACI Consortium
    • , Shaun Purcell
    • , Eli Stahl
    • , Sara Lindstrom
    • , John R B Perry
    • , Yukinori Okada
    • , Soumya Raychaudhuri
    • , Mark J Daly
    • , Nick Patterson
    • , Benjamin M Neale
    •  &  Alkes L Price
  • Nature Communications | Article | open

    Cell-to-cell communication relies upon interactions between secreted ligands and cell surface receptors. Here, Ramilowski et al. present a draft cell-to-cell communication network based on expression of ligand-receptor pairs in 144 different human cell types.

    • Jordan A. Ramilowski
    • , Tatyana Goldberg
    • , Jayson Harshbarger
    • , Edda Kloppmann
    • , Marina Lizio
    • , Venkata P. Satagopam
    • , Masayoshi Itoh
    • , Hideya Kawaji
    • , Piero Carninci
    • , Burkhard Rost
    •  &  Alistair R. R. Forrest
  • Nature Communications | Article

    Body plan complexity is associated with the number of different cell types, yet the processes that create this diversity are unclear. Here the authors use transcriptomics to test the hypothesis that unlike cancer cells, novel normal cell types arise through sub-specialization of an ancestral cell type.

    • Cong Liang
    • , the FANTOM Consortium
    • , Alistair R.R. Forrest
    •  &  Günter P. Wagner
  • Nature Genetics | Article

    Piero Carninci and colleagues report the discovery of a large class of noncoding RNAs, non-annotated stem cell transcripts (NASTs), which are implicated in the regulation of stem cell properties. The authors identify 8,873 mouse and 3,042 human NASTs and functionally validate 4 as having an important role in the maintenance of pluripotency.

    • Alexandre Fort
    • , Kosuke Hashimoto
    • , Daisuke Yamada
    • , Md Salimullah
    • , Chaman A Keya
    • , Alka Saxena
    • , Alessandro Bonetti
    • , Irina Voineagu
    • , Nicolas Bertin
    • , Anton Kratz
    • , Yukihiko Noro
    • , Chee-Hong Wong
    • , Michiel de Hoon
    • , Robin Andersson
    • , Albin Sandelin
    • , Harukazu Suzuki
    • , Chia-Lin Wei
    • , Haruhiko Koseki
    • , The FANTOM Consortium
    • , Yuki Hasegawa
    • , Alistair R R Forrest
    •  &  Piero Carninci
  • Nature | Article

    A study from the FANTOM consortium using single-molecule cDNA sequencing of transcription start sites and their usage in human and mouse primary cells, cell lines and tissues reveals insights into the specificity and diversity of transcription patterns across different mammalian cell types.

    • The FANTOM Consortium and the RIKEN PMI and CLST (DGT)
    • , Alistair R. R. Forrest
    • , Hideya Kawaji
    • , Michael Rehli
    • , J. Kenneth Baillie
    • , Michiel J. L. de Hoon
    • , Vanja Haberle
    • , Timo Lassmann
    • , Ivan V. Kulakovskiy
    • , Marina Lizio
    • , Masayoshi Itoh
    • , Robin Andersson
    • , Christopher J. Mungall
    • , Terrence F. Meehan
    • , Sebastian Schmeier
    • , Nicolas Bertin
    • , Mette Jørgensen
    • , Emmanuel Dimont
    • , Erik Arner
    • , Christian Schmidl
    • , Ulf Schaefer
    • , Yulia A. Medvedeva
    • , Charles Plessy
    • , Morana Vitezic
    • , Jessica Severin
    • , Colin A. Semple
    • , Yuri Ishizu
    • , Robert S. Young
    • , Margherita Francescatto
    • , Intikhab Alam
    • , Davide Albanese
    • , Gabriel M. Altschuler
    • , Takahiro Arakawa
    • , John A. C. Archer
    • , Peter Arner
    • , Magda Babina
    • , Sarah Rennie
    • , Piotr J. Balwierz
    • , Anthony G. Beckhouse
    • , Swati Pradhan-Bhatt
    • , Judith A. Blake
    • , Antje Blumenthal
    • , Beatrice Bodega
    • , Alessandro Bonetti
    • , James Briggs
    • , Frank Brombacher
    • , A. Maxwell Burroughs
    • , Andrea Califano
    • , Carlo V. Cannistraci
    • , Daniel Carbajo
    • , Yun Chen
    • , Marco Chierici
    • , Yari Ciani
    • , Hans C. Clevers
    • , Emiliano Dalla
    • , Carrie A. Davis
    • , Michael Detmar
    • , Alexander D. Diehl
    • , Taeko Dohi
    • , Finn Drabløs
    • , Albert S. B. Edge
    • , Matthias Edinger
    • , Karl Ekwall
    • , Mitsuhiro Endoh
    • , Hideki Enomoto
    • , Michela Fagiolini
    • , Lynsey Fairbairn
    • , Hai Fang
    • , Mary C. Farach-Carson
    • , Geoffrey J. Faulkner
    • , Alexander V. Favorov
    • , Malcolm E. Fisher
    • , Martin C. Frith
    • , Rie Fujita
    • , Shiro Fukuda
    • , Cesare Furlanello
    • , Masaaki Furuno
    • , Jun-ichi Furusawa
    • , Teunis B. Geijtenbeek
    • , Andrew P. Gibson
    • , Thomas Gingeras
    • , Daniel Goldowitz
    • , Julian Gough
    • , Sven Guhl
    • , Reto Guler
    • , Stefano Gustincich
    • , Thomas J. Ha
    • , Masahide Hamaguchi
    • , Mitsuko Hara
    • , Matthias Harbers
    • , Jayson Harshbarger
    • , Akira Hasegawa
    • , Yuki Hasegawa
    • , Takehiro Hashimoto
    • , Meenhard Herlyn
    • , Kelly J. Hitchens
    • , Shannan J. Ho Sui
    • , Oliver M. Hofmann
    • , Ilka Hoof
    • , Fumi Hori
    • , Lukasz Huminiecki
    • , Kei Iida
    • , Tomokatsu Ikawa
    • , Boris R. Jankovic
    • , Hui Jia
    • , Anagha Joshi
    • , Giuseppe Jurman
    • , Bogumil Kaczkowski
    • , Chieko Kai
    • , Kaoru Kaida
    • , Ai Kaiho
    • , Kazuhiro Kajiyama
    • , Mutsumi Kanamori-Katayama
    • , Artem S. Kasianov
    • , Takeya Kasukawa
    • , Shintaro Katayama
    • , Sachi Kato
    • , Shuji Kawaguchi
    • , Hiroshi Kawamoto
    • , Yuki I. Kawamura
    • , Tsugumi Kawashima
    • , Judith S. Kempfle
    • , Tony J. Kenna
    • , Juha Kere
    • , Levon M. Khachigian
    • , Toshio Kitamura
    • , S. Peter Klinken
    • , Alan J. Knox
    • , Miki Kojima
    • , Soichi Kojima
    • , Naoto Kondo
    • , Haruhiko Koseki
    • , Shigeo Koyasu
    • , Sarah Krampitz
    • , Atsutaka Kubosaki
    • , Andrew T. Kwon
    • , Jeroen F. J. Laros
    • , Weonju Lee
    • , Andreas Lennartsson
    • , Kang Li
    • , Berit Lilje
    • , Leonard Lipovich
    • , Alan Mackay-sim
    • , Ri-ichiroh Manabe
    • , Jessica C. Mar
    • , Benoit Marchand
    • , Anthony Mathelier
    • , Niklas Mejhert
    • , Alison Meynert
    • , Yosuke Mizuno
    • , David A. de Lima Morais
    • , Hiromasa Morikawa
    • , Mitsuru Morimoto
    • , Kazuyo Moro
    • , Efthymios Motakis
    • , Hozumi Motohashi
    • , Christine L. Mummery
    • , Mitsuyoshi Murata
    • , Sayaka Nagao-Sato
    • , Yutaka Nakachi
    • , Fumio Nakahara
    • , Toshiyuki Nakamura
    • , Yukio Nakamura
    • , Kenichi Nakazato
    • , Erik van Nimwegen
    • , Noriko Ninomiya
    • , Hiromi Nishiyori
    • , Shohei Noma
    • , Tadasuke Nozaki
    • , Soichi Ogishima
    • , Naganari Ohkura
    • , Hiroko Ohmiya
    • , Hiroshi Ohno
    • , Mitsuhiro Ohshima
    • , Mariko Okada-Hatakeyama
    • , Yasushi Okazaki
    • , Valerio Orlando
    • , Dmitry A. Ovchinnikov
    • , Arnab Pain
    • , Robert Passier
    • , Margaret Patrikakis
    • , Helena Persson
    • , Silvano Piazza
    • , James G. D. Prendergast
    • , Owen J. L. Rackham
    • , Jordan A. Ramilowski
    • , Mamoon Rashid
    • , Timothy Ravasi
    • , Patrizia Rizzu
    • , Marco Roncador
    • , Sugata Roy
    • , Morten B. Rye
    • , Eri Saijyo
    • , Antti Sajantila
    • , Akiko Saka
    • , Shimon Sakaguchi
    • , Mizuho Sakai
    • , Hiroki Sato
    • , Hironori Satoh
    • , Suzana Savvi
    • , Alka Saxena
    • , Claudio Schneider
    • , Erik A. Schultes
    • , Gundula G. Schulze-Tanzil
    • , Anita Schwegmann
    • , Thierry Sengstag
    • , Guojun Sheng
    • , Hisashi Shimoji
    • , Yishai Shimoni
    • , Jay W. Shin
    • , Christophe Simon
    • , Daisuke Sugiyama
    • , Takaaki Sugiyama
    • , Masanori Suzuki
    • , Naoko Suzuki
    • , Rolf K. Swoboda
    • , Peter A. C. ’t Hoen
    • , Michihira Tagami
    • , Naoko Takahashi
    • , Jun Takai
    • , Hiroshi Tanaka
    • , Hideki Tatsukawa
    • , Zuotian Tatum
    • , Mark Thompson
    • , Hiroo Toyoda
    • , Tetsuro Toyoda
    • , Eivind Valen
    • , Marc van de Wetering
    • , Linda M. van den Berg
    • , Roberto Verardo
    • , Dipti Vijayan
    • , Ilya E. Vorontsov
    • , Wyeth W. Wasserman
    • , Shoko Watanabe
    • , Christine A. Wells
    • , Louise N. Winteringham
    • , Ernst Wolvetang
    • , Emily J. Wood
    • , Yoko Yamaguchi
    • , Masayuki Yamamoto
    • , Misako Yoneda
    • , Yohei Yonekura
    • , Shigehiro Yoshida
    • , Susan E. Zabierowski
    • , Peter G. Zhang
    • , Xiaobei Zhao
    • , Silvia Zucchelli
    • , Kim M. Summers
    • , Harukazu Suzuki
    • , Carsten O. Daub
    • , Jun Kawai
    • , Peter Heutink
    • , Winston Hide
    • , Tom C. Freeman
    • , Boris Lenhard
    • , Vladimir B. Bajic
    • , Martin S. Taylor
    • , Vsevolod J. Makeev
    • , Albin Sandelin
    • , David A. Hume
    • , Piero Carninci
    •  &  Yoshihide Hayashizaki
  • Nature | Article

    Using the FANTOM5 CAGE expression atlas, the authors show that bidirectional capped RNAs are a signature feature of active enhancers and identify over 40,000 enhancer candidates from over 800 human cell and tissue samples across the whole human body.

    • Robin Andersson
    • , Claudia Gebhard
    • , Irene Miguel-Escalada
    • , Ilka Hoof
    • , Jette Bornholdt
    • , Mette Boyd
    • , Yun Chen
    • , Xiaobei Zhao
    • , Christian Schmidl
    • , Takahiro Suzuki
    • , Evgenia Ntini
    • , Erik Arner
    • , Eivind Valen
    • , Kang Li
    • , Lucia Schwarzfischer
    • , Dagmar Glatz
    • , Johanna Raithel
    • , Berit Lilje
    • , Nicolas Rapin
    • , Frederik Otzen Bagger
    • , Mette Jørgensen
    • , Peter Refsing Andersen
    • , Nicolas Bertin
    • , Owen Rackham
    • , A. Maxwell Burroughs
    • , J. Kenneth Baillie
    • , Yuri Ishizu
    • , Yuri Shimizu
    • , Erina Furuhata
    • , Shiori Maeda
    • , Yutaka Negishi
    • , Christopher J. Mungall
    • , Terrence F. Meehan
    • , Timo Lassmann
    • , Masayoshi Itoh
    • , Hideya Kawaji
    • , Naoto Kondo
    • , Jun Kawai
    • , Andreas Lennartsson
    • , Carsten O. Daub
    • , Peter Heutink
    • , David A. Hume
    • , Torben Heick Jensen
    • , Harukazu Suzuki
    • , Yoshihide Hayashizaki
    • , Ferenc Müller
    • , The FANTOM Consortium
    • , Alistair R. R. Forrest
    • , Piero Carninci
    • , Michael Rehli
    •  &  Albin Sandelin