title: A promoter-level mammalian expression atlas.
abstract: Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.
authors.forename: Alistair R R
authors.initials: AR
authors.lastname: Forrest
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Michael
authors.initials: M
authors.lastname: Rehli
authors.forename: J Kenneth
authors.initials: JK
authors.lastname: Baillie
authors.forename: Michiel J L
authors.initials: MJ
authors.lastname: de Hoon
authors.forename: Vanja
authors.initials: V
authors.lastname: Haberle
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Kulakovskiy
authors.forename: Marina
authors.initials: M
authors.lastname: Lizio
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Itoh
authors.forename: Robin
authors.initials: R
authors.lastname: Andersson
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.forename: Terrence F
authors.initials: TF
authors.lastname: Meehan
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schmeier
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.forename: Mette
authors.initials: M
authors.lastname: Jørgensen
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Dimont
authors.forename: Erik
authors.initials: E
authors.lastname: Arner
authors.forename: Christian
authors.initials: C
authors.lastname: Schmidl
authors.forename: Ulf
authors.initials: U
authors.lastname: Schaefer
authors.forename: Yulia A
authors.initials: YA
authors.lastname: Medvedeva
authors.forename: Charles
authors.initials: C
authors.lastname: Plessy
authors.forename: Morana
authors.initials: M
authors.lastname: Vitezic
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Colin  A
authors.initials: C
authors.lastname: Semple
authors.forename: Yuri
authors.initials: Y
authors.lastname: Ishizu
authors.forename: Robert S
authors.initials: RS
authors.lastname: Young
authors.forename: Margherita
authors.initials: M
authors.lastname: Francescatto
authors.forename: Intikhab
authors.initials: I
authors.lastname: Alam
authors.forename: Davide
authors.initials: D
authors.lastname: Albanese
authors.forename: Gabriel M
authors.initials: GM
authors.lastname: Altschuler
authors.forename: Takahiro
authors.initials: T
authors.lastname: Arakawa
authors.forename: John A C
authors.initials: JA
authors.lastname: Archer
authors.forename: Peter
authors.initials: P
authors.lastname: Arner
authors.forename: Magda
authors.initials: M
authors.lastname: Babina
authors.forename: Sarah
authors.initials: S
authors.lastname: Rennie
authors.forename: Piotr J
authors.initials: PJ
authors.lastname: Balwierz
authors.forename: Anthony G
authors.initials: AG
authors.lastname: Beckhouse
authors.forename: Swati
authors.initials: S
authors.lastname: Pradhan-Bhatt
authors.forename: Judith A
authors.initials: JA
authors.lastname: Blake
authors.forename: Antje
authors.initials: A
authors.lastname: Blumenthal
authors.forename: Beatrice
authors.initials: B
authors.lastname: Bodega
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bonetti
authors.forename: James
authors.initials: J
authors.lastname: Briggs
authors.forename: Frank
authors.initials: F
authors.lastname: Brombacher
authors.forename: A Maxwell
authors.initials: AM
authors.lastname: Burroughs
authors.forename: Andrea
authors.initials: A
authors.lastname: Califano
authors.forename: Carlo V
authors.initials: CV
authors.lastname: Cannistraci
authors.forename: Daniel
authors.initials: D
authors.lastname: Carbajo
authors.forename: Yun
authors.initials: Y
authors.lastname: Chen
authors.forename: Marco
authors.initials: M
authors.lastname: Chierici
authors.forename: Yari
authors.initials: Y
authors.lastname: Ciani
authors.forename: Hans C
authors.initials: HC
authors.lastname: Clevers
authors.forename: Emiliano
authors.initials: E
authors.lastname: Dalla
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Michael
authors.initials: M
authors.lastname: Detmar
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Diehl
authors.forename: Taeko
authors.initials: T
authors.lastname: Dohi
authors.forename: Finn
authors.initials: F
authors.lastname: Drabløs
authors.forename: Albert S B
authors.initials: AS
authors.lastname: Edge
authors.forename: Matthias
authors.initials: M
authors.lastname: Edinger
authors.forename: Karl
authors.initials: K
authors.lastname: Ekwall
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Endoh
authors.forename: Hideki
authors.initials: H
authors.lastname: Enomoto
authors.forename: Michela
authors.initials: M
authors.lastname: Fagiolini
authors.forename: Lynsey
authors.initials: L
authors.lastname: Fairbairn
authors.forename: Hai
authors.initials: H
authors.lastname: Fang
authors.forename: Mary C
authors.initials: MC
authors.lastname: Farach-Carson
authors.forename: Geoffrey J
authors.initials: GJ
authors.lastname: Faulkner
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Favorov
authors.forename: Malcolm E
authors.initials: ME
authors.lastname: Fisher
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
authors.forename: Rie
authors.initials: R
authors.lastname: Fujita
authors.forename: Shiro
authors.initials: S
authors.lastname: Fukuda
authors.forename: Cesare
authors.initials: C
authors.lastname: Furlanello
authors.forename: Masaaki
authors.initials: M
authors.lastname: Furino
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Furusawa
authors.forename: Teunis B
authors.initials: TB
authors.lastname: Geijtenbeek
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Gibson
authors.forename: Thomas
authors.initials: T
authors.lastname: Gingeras
authors.forename: Daniel
authors.initials: D
authors.lastname: Goldowitz
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.forename: Sven
authors.initials: S
authors.lastname: Guhl
authors.forename: Reto
authors.initials: R
authors.lastname: Guler
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Ha
authors.forename: Masahide
authors.initials: M
authors.lastname: Hamaguchi
authors.forename: Mitsuko
authors.initials: M
authors.lastname: Hara
authors.forename: Matthias
authors.initials: M
authors.lastname: Harbers
authors.forename: Jayson
authors.initials: J
authors.lastname: Harshbarger
authors.forename: Akira
authors.initials: A
authors.lastname: Hasegawa
authors.forename: Yuki
authors.initials: Y
authors.lastname: Hasegawa
authors.forename: Takehiro
authors.initials: T
authors.lastname: Hashimoto
authors.forename: Meenhard
authors.initials: M
authors.lastname: Herlyn
authors.forename: Kelly J
authors.initials: KJ
authors.lastname: Hitchens
authors.forename: Shannan J
authors.initials: SJ
authors.lastname: Ho Sui
authors.forename: Oliver M
authors.initials: OM
authors.lastname: Hofmann
authors.forename: Ilka
authors.initials: I
authors.lastname: Hoof
authors.forename: Furni
authors.initials: F
authors.lastname: Hori
authors.forename: Lukasz
authors.initials: L
authors.lastname: Huminiecki
authors.forename: Kei
authors.initials: K
authors.lastname: Iida
authors.forename: Tomokatsu
authors.initials: T
authors.lastname: Ikawa
authors.forename: Boris R
authors.initials: BR
authors.lastname: Jankovic
authors.forename: Hui
authors.initials: H
authors.lastname: Jia
authors.forename: Anagha
authors.initials: A
authors.lastname: Joshi
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Jurman
authors.forename: Bogumil
authors.initials: B
authors.lastname: Kaczkowski
authors.forename: Chieko
authors.initials: C
authors.lastname: Kai
authors.forename: Kaoru
authors.initials: K
authors.lastname: Kaida
authors.forename: Ai
authors.initials: A
authors.lastname: Kaiho
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Kajiyama
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Kanamori-Katayama
authors.forename: Artem S
authors.initials: AS
authors.lastname: Kasianov
authors.forename: Takeya
authors.initials: T
authors.lastname: Kasukawa
authors.forename: Shintaro
authors.initials: S
authors.lastname: Katayama
authors.forename: Sachi
authors.initials: S
authors.lastname: Kato
authors.forename: Shuji
authors.initials: S
authors.lastname: Kawaguchi
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kawamoto
authors.forename: Yuki I
authors.initials: YI
authors.lastname: Kawamura
authors.forename: Tsugumi
authors.initials: T
authors.lastname: Kawashima
authors.forename: Judith S
authors.initials: JS
authors.lastname: Kempfle
authors.forename: Tony J
authors.initials: TJ
authors.lastname: Kenna
authors.forename: Juha
authors.initials: J
authors.lastname: Kere
authors.forename: Levon M
authors.initials: LM
authors.lastname: Khachigian
authors.forename: Toshio
authors.initials: T
authors.lastname: Kitamura
authors.forename: S Peter
authors.initials: SP
authors.lastname: Klinken
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Knox
authors.forename: Miki
authors.initials: M
authors.lastname: Kojima
authors.forename: Soichi
authors.initials: S
authors.lastname: Kojima
authors.forename: Naoto
authors.initials: N
authors.lastname: Kondo
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Koseki
authors.forename: Shigeo
authors.initials: S
authors.lastname: Koyasu
authors.forename: Sarah
authors.initials: S
authors.lastname: Krampitz
authors.forename: Atsutaka
authors.initials: A
authors.lastname: Kubosaki
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Kwon
authors.forename: Jeroen F J
authors.initials: JF
authors.lastname: Laros
authors.forename: Weonju
authors.initials: W
authors.lastname: Lee
authors.forename: Andreas
authors.initials: A
authors.lastname: Lennartsson
authors.forename: Kang
authors.initials: K
authors.lastname: Li
authors.forename: Berit
authors.initials: B
authors.lastname: Lilje
authors.forename: Leonard
authors.initials: L
authors.lastname: Lipovich
authors.forename: Alan
authors.initials: A
authors.lastname: Mackay-Sim
authors.forename: Ri-ichiroh
authors.initials: R
authors.lastname: Manabe
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Mar
authors.forename: Benoit
authors.initials: B
authors.lastname: Marchand
authors.forename: Anthony
authors.initials: A
authors.lastname: Mathelier
authors.forename: Niklas
authors.initials: N
authors.lastname: Mejhert
authors.forename: Alison
authors.initials: A
authors.lastname: Meynert
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Mizuno
authors.forename: David A
authors.initials: DA
authors.lastname: de Lima Morais
authors.forename: Hiromasa
authors.initials: H
authors.lastname: Morikawa
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Morimoto
authors.forename: Kazuyo
authors.initials: K
authors.lastname: Moro
authors.forename: Efthymios
authors.initials: E
authors.lastname: Motakis
authors.forename: Hozumi
authors.initials: H
authors.lastname: Motohashi
authors.forename: Christine L
authors.initials: CL
authors.lastname: Mummery
authors.forename: Mitsuyoshi
authors.initials: M
authors.lastname: Murata
authors.forename: Sayaka
authors.initials: S
authors.lastname: Nagao-Sato
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authors.initials: Y
authors.lastname: Nakachi
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authors.initials: F
authors.lastname: Nakahara
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Nakamura
authors.forename: Yukio
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Kenichi
authors.initials: K
authors.lastname: Nakazato
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
authors.forename: Noriko
authors.initials: N
authors.lastname: Ninomiya
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authors.initials: H
authors.lastname: Nishiyori
authors.forename: Shohei
authors.initials: S
authors.lastname: Noma
authors.forename: Shohei
authors.initials: S
authors.lastname: Noma
authors.forename: Tadasuke
authors.initials: T
authors.lastname: Noazaki
authors.forename: Soichi
authors.initials: S
authors.lastname: Ogishima
authors.forename: Naganari
authors.initials: N
authors.lastname: Ohkura
authors.forename: Hiroko
authors.initials: H
authors.lastname: Ohimiya
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ohno
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Ohshima
authors.forename: Mariko
authors.initials: M
authors.lastname: Okada-Hatakeyama
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okazaki
authors.forename: Valerio
authors.initials: V
authors.lastname: Orlando
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Ovchinnikov
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.forename: Robert
authors.initials: R
authors.lastname: Passier
authors.forename: Margaret
authors.initials: M
authors.lastname: Patrikakis
authors.forename: Helena
authors.initials: H
authors.lastname: Persson
authors.forename: Silvano
authors.initials: S
authors.lastname: Piazza
authors.forename: James G D
authors.initials: JG
authors.lastname: Prendergast
authors.forename: Owen J L
authors.initials: OJ
authors.lastname: Rackham
authors.forename: Jordan A
authors.initials: JA
authors.lastname: Ramilowski
authors.forename: Mamoon
authors.initials: M
authors.lastname: Rashid
authors.forename: Timothy
authors.initials: T
authors.lastname: Ravasi
authors.forename: Patrizia
authors.initials: P
authors.lastname: Rizzu
authors.forename: Marco
authors.initials: M
authors.lastname: Roncador
authors.forename: Sugata
authors.initials: S
authors.lastname: Roy
authors.forename: Morten B
authors.initials: MB
authors.lastname: Rye
authors.forename: Eri
authors.initials: E
authors.lastname: Saijyo
authors.forename: Antti
authors.initials: A
authors.lastname: Sajantila
authors.forename: Akiko
authors.initials: A
authors.lastname: Saka
authors.forename: Shimon
authors.initials: S
authors.lastname: Sakaguchi
authors.forename: Mizuho
authors.initials: M
authors.lastname: Sakai
authors.forename: Hiroki
authors.initials: H
authors.lastname: Sato
authors.forename: Suzana
authors.initials: S
authors.lastname: Savvi
authors.forename: Alka
authors.initials: A
authors.lastname: Saxena
authors.forename: Claudio
authors.initials: C
authors.lastname: Schneider
authors.forename: Erik A
authors.initials: EA
authors.lastname: Schultes
authors.forename: Gundula G
authors.initials: GG
authors.lastname: Schulze-Tanzil
authors.forename: Anita
authors.initials: A
authors.lastname: Schwegmann
authors.forename: Thierry
authors.initials: T
authors.lastname: Sengstag
authors.forename: Guojun
authors.initials: G
authors.lastname: Sheng
authors.forename: Hisashi
authors.initials: H
authors.lastname: Shimoji
authors.forename: Yishai
authors.initials: Y
authors.lastname: Shimoni
authors.forename: Jay W
authors.initials: JW
authors.lastname: Shin
authors.forename: Christophe
authors.initials: C
authors.lastname: Simon
authors.forename: Daisuke
authors.initials: D
authors.lastname: Sugiyama
authors.forename: Takaai
authors.initials: T
authors.lastname: Sugiyama
authors.forename: Masanori
authors.initials: M
authors.lastname: Suzuki
authors.forename: Naoko
authors.initials: N
authors.lastname: Suzuki
authors.forename: Rolf K
authors.initials: RK
authors.lastname: Swoboda
authors.forename: Peter A C
authors.initials: PA
authors.lastname: 't Hoen
authors.forename: Michihira
authors.initials: M
authors.lastname: Tagami
authors.forename: Naoko
authors.initials: N
authors.lastname: Takahashi
authors.forename: Jun
authors.initials: J
authors.lastname: Takai
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tanaka
authors.forename: Hideki
authors.initials: H
authors.lastname: Tatsukawa
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authors.initials: Z
authors.lastname: Tatum
authors.forename: Mark
authors.initials: M
authors.lastname: Thompson
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authors.initials: H
authors.lastname: Toyodo
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
authors.forename: Elvind
authors.initials: E
authors.lastname: Valen
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authors.initials: M
authors.lastname: van de Wetering
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authors.initials: LM
authors.lastname: van den Berg
authors.forename: Roberto
authors.initials: R
authors.lastname: Verado
authors.forename: Dipti
authors.initials: D
authors.lastname: Vijayan
authors.forename: Ilya E
authors.initials: IE
authors.lastname: Vorontsov
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
authors.forename: Shoko
authors.initials: S
authors.lastname: Watanabe
authors.forename: Christine A
authors.initials: CA
authors.lastname: Wells
authors.forename: Louise N
authors.initials: LN
authors.lastname: Winteringham
authors.forename: Ernst
authors.initials: E
authors.lastname: Wolvetang
authors.forename: Emily J
authors.initials: EJ
authors.lastname: Wood
authors.forename: Yoko
authors.initials: Y
authors.lastname: Yamaguchi
authors.forename: Masayuki
authors.initials: M
authors.lastname: Yamamoto
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authors.initials: M
authors.lastname: Yoneda
authors.forename: Yohei
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authors.lastname: Yonekura
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authors.initials: S
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authors.lastname: Zhang
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authors.initials: X
authors.lastname: Zhao
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authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
authors.forename: Carsten O
authors.initials: CO
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authors.lastname: Hide
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authors.forename: Vladimir B
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authors.lastname: Bajic
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authors.lastname: Taylor
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authors.initials: VJ
authors.lastname: Makeev
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
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authors.initials: DA
authors.lastname: Hume
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D002460:Cell Line; D002478:Cells, Cultured; D016000:Cluster Analysis; D017124:Conserved Sequence / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D020043:Genes, Essential / Q000235:genetics; D016678:Genome / Q000235:genetics; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D009928:Organ Specificity; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors