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A promoter-level mammalian expression atlas
- Source :
- Nature, 507(7493), 462-70. Nature Publishing Group, Nature, 507(7493), 462-+. Nature Publishing Group, Forrest, A R R, Kawaji, H, Rehli, M, Baillie, J K, de Hoon, M J L, Haberle, V, Lassmann, T, Kulakovskiy, I V, Lizio, M, Itoh, M, Andersson, R, Mungall, C J, Meehan, T F, Schmeier, S, Bertin, N, Jorgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, Y A, Plessy, C, Vitezic, M, Severin, J, Semple, C A, Ishizu, Y, Young, R S, Francescatto, M, Alam, I, Albanese, D, Altschuler, G M, Arakawa, T, Archer, J A C, Arner, P, Babina, M, Rennie, S, Balwierz, P J, Beckhouse, A G, Pradhan-Bhatt, S, Blake, J A, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, A M, Califano, A, Cannistraci, C V, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, H C, Dalla, E, Davis, C A, Detmar, M, Diehl, A D, Dohi, T, Drablos, F, Edge, A S B, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach-Carson, M C, Faulkner, G J, Favorov, A V, Fisher, M E, Frith, M C, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, T B, Gibson, A P, Gingeras, T, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, S, Ha, T J, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, M, Hitchens, K J, Sui, S J H, Hofmann, O M, Hoof, I, Hori, F, Rizzu, P, Heutink, P, Carninci, P & Hayashizaki, Y 2014, ' A promoter-level mammalian expression atlas ', Nature, vol. 507, no. 7493, pp. 462-470 . https://doi.org/10.1038/nature13182, Nature, 507(7493), 462-470. Nature Publishing Group, Nature, 507(7493), 462, BASE-Bielefeld Academic Search Engine
- Publication Year :
- 2014
-
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.
- Subjects :
- Transcription, Genetic
Cells
Messenger
Gene regulatory network
Mammalian promoter database
Biology
Article
Cell Line
Promoter Regions
Mice
Open Reading Frames
Essential
Atlases as Topic
Genetic
Animals
Cluster Analysis
Humans
Gene Regulatory Networks
RNA, Messenger
Promoter Regions, Genetic
Gene
Transcription factor
Cells, Cultured
Conserved Sequence
Genetics
Regulation of gene expression
Cultured
Multidisciplinary
Genes, Essential
Genome
Promoter
Molecular Sequence Annotation
Cap analysis gene expression
Genes
Gene Expression Regulation
Organ Specificity
Transcription Factors
Transcription Initiation Site
Transcriptome
RNA
Human genome
Transcription
Subjects
Details
- Language :
- English
- ISSN :
- 00280836
- Volume :
- 507
- Issue :
- 7493
- Database :
- OpenAIRE
- Journal :
- Nature
- Accession number :
- edsair.doi.dedup.....00d8c6cbaf9d628ba60c42afae558f77