A promoter-level mammalian expression atlas

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A promoter-level mammalian expression atlas. / Forrest, Alistair R R; Kawaji, Hideya; Rehli, Michael; Baillie, J Kenneth; de Hoon, Michiel J L; Haberle, Vanja; Lassmann, Timo; Kulakovskiy, Ivan V; Lizio, Marina; Itoh, Masayoshi; Andersson, Robin; Mungall, Christopher J; Meehan, Terrence F; Schmeier, Sebastian; Bertin, Nicolas; Jørgensen, Mette; Dimont, Emmanuel; Arner, Erik; Schmidl, Christian; Schaefer, Ulf; Medvedeva, Yulia A; Plessy, Charles; Vitezic, Morana; Severin, Jessica; Semple, Colin A; Ishizu, Yuri; Young, Robert S; Francescatto, Margherita; Alam, Intikhab; Albanese, Davide; Altschuler, Gabriel M; Arakawa, Takahiro; Archer, John A C; Arner, Peter; Babina, Magda; Rennie, Sarah; Balwierz, Piotr J; Beckhouse, Anthony G; Pradhan-Bhatt, Swati; Blake, Judith A; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Burroughs, A Maxwell; Califano, Andrea; Lennartsson, Andreas; Persson, Helena; Thompson, Mark; FANTOM Consortium and the RIKEN PMI and CLST (DGT).

In: Nature, Vol. 507, No. 7493, 27.03.2014, p. 462-70.

Research output: Contribution to journalArticle

Harvard

Forrest, ARR, Kawaji, H, Rehli, M, Baillie, JK, de Hoon, MJL, Haberle, V, Lassmann, T, Kulakovskiy, IV, Lizio, M, Itoh, M, Andersson, R, Mungall, CJ, Meehan, TF, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, YA, Plessy, C, Vitezic, M, Severin, J, Semple, CA, Ishizu, Y, Young, RS, Francescatto, M, Alam, I, Albanese, D, Altschuler, GM, Arakawa, T, Archer, JAC, Arner, P, Babina, M, Rennie, S, Balwierz, PJ, Beckhouse, AG, Pradhan-Bhatt, S, Blake, JA, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, AM, Califano, A, Lennartsson, A, Persson, H, Thompson, M & FANTOM Consortium and the RIKEN PMI and CLST (DGT) 2014, 'A promoter-level mammalian expression atlas', Nature, vol. 507, no. 7493, pp. 462-70. https://doi.org/10.1038/nature13182

APA

Forrest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., de Hoon, M. J. L., Haberle, V., ... FANTOM Consortium and the RIKEN PMI and CLST (DGT) (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462-70. https://doi.org/10.1038/nature13182

CBE

Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JAC, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Lennartsson A, Persson H, Thompson M, FANTOM Consortium and the RIKEN PMI and CLST (DGT). 2014. A promoter-level mammalian expression atlas. Nature. 507(7493):462-70. https://doi.org/10.1038/nature13182

MLA

Forrest, Alistair R R et al. "A promoter-level mammalian expression atlas". Nature. 2014, 507(7493). 462-70. https://doi.org/10.1038/nature13182

Vancouver

Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. https://doi.org/10.1038/nature13182

Author

Forrest, Alistair R R ; Kawaji, Hideya ; Rehli, Michael ; Baillie, J Kenneth ; de Hoon, Michiel J L ; Haberle, Vanja ; Lassmann, Timo ; Kulakovskiy, Ivan V ; Lizio, Marina ; Itoh, Masayoshi ; Andersson, Robin ; Mungall, Christopher J ; Meehan, Terrence F ; Schmeier, Sebastian ; Bertin, Nicolas ; Jørgensen, Mette ; Dimont, Emmanuel ; Arner, Erik ; Schmidl, Christian ; Schaefer, Ulf ; Medvedeva, Yulia A ; Plessy, Charles ; Vitezic, Morana ; Severin, Jessica ; Semple, Colin A ; Ishizu, Yuri ; Young, Robert S ; Francescatto, Margherita ; Alam, Intikhab ; Albanese, Davide ; Altschuler, Gabriel M ; Arakawa, Takahiro ; Archer, John A C ; Arner, Peter ; Babina, Magda ; Rennie, Sarah ; Balwierz, Piotr J ; Beckhouse, Anthony G ; Pradhan-Bhatt, Swati ; Blake, Judith A ; Blumenthal, Antje ; Bodega, Beatrice ; Bonetti, Alessandro ; Briggs, James ; Brombacher, Frank ; Burroughs, A Maxwell ; Califano, Andrea ; Lennartsson, Andreas ; Persson, Helena ; Thompson, Mark ; FANTOM Consortium and the RIKEN PMI and CLST (DGT). / A promoter-level mammalian expression atlas. In: Nature. 2014 ; Vol. 507, No. 7493. pp. 462-70.

RIS

TY - JOUR

T1 - A promoter-level mammalian expression atlas

AU - Forrest, Alistair R R

AU - Kawaji, Hideya

AU - Rehli, Michael

AU - Baillie, J Kenneth

AU - de Hoon, Michiel J L

AU - Haberle, Vanja

AU - Lassmann, Timo

AU - Kulakovskiy, Ivan V

AU - Lizio, Marina

AU - Itoh, Masayoshi

AU - Andersson, Robin

AU - Mungall, Christopher J

AU - Meehan, Terrence F

AU - Schmeier, Sebastian

AU - Bertin, Nicolas

AU - Jørgensen, Mette

AU - Dimont, Emmanuel

AU - Arner, Erik

AU - Schmidl, Christian

AU - Schaefer, Ulf

AU - Medvedeva, Yulia A

AU - Plessy, Charles

AU - Vitezic, Morana

AU - Severin, Jessica

AU - Semple, Colin A

AU - Ishizu, Yuri

AU - Young, Robert S

AU - Francescatto, Margherita

AU - Alam, Intikhab

AU - Albanese, Davide

AU - Altschuler, Gabriel M

AU - Arakawa, Takahiro

AU - Archer, John A C

AU - Arner, Peter

AU - Babina, Magda

AU - Rennie, Sarah

AU - Balwierz, Piotr J

AU - Beckhouse, Anthony G

AU - Pradhan-Bhatt, Swati

AU - Blake, Judith A

AU - Blumenthal, Antje

AU - Bodega, Beatrice

AU - Bonetti, Alessandro

AU - Briggs, James

AU - Brombacher, Frank

AU - Burroughs, A Maxwell

AU - Califano, Andrea

AU - Lennartsson, Andreas

AU - Persson, Helena

AU - Thompson, Mark

AU - FANTOM Consortium and the RIKEN PMI and CLST (DGT)

PY - 2014/3/27

Y1 - 2014/3/27

N2 - 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.

AB - 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.

KW - Animals

KW - Atlases as Topic

KW - Cell Line

KW - Cells, Cultured

KW - Cluster Analysis

KW - Conserved Sequence

KW - Gene Expression Regulation

KW - Gene Regulatory Networks

KW - Genes, Essential

KW - Genome

KW - Humans

KW - Mice

KW - Molecular Sequence Annotation

KW - Open Reading Frames

KW - Organ Specificity

KW - Promoter Regions, Genetic

KW - RNA, Messenger

KW - Transcription Factors

KW - Transcription Initiation Site

KW - Transcription, Genetic

KW - Transcriptome

U2 - 10.1038/nature13182

DO - 10.1038/nature13182

M3 - Article

VL - 507

SP - 462

EP - 470

JO - Nature

T2 - Nature

JF - Nature

SN - 0028-0836

IS - 7493

ER -