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.

FANTOM5 organizers published a Comment announcing the launch of this collection and have been interviewed on their contributions to FANTOM5.

Data Descriptors

Design Type(s) species comparison design • organism part comparison design • cell type comparison design Measurement Type(s) DNA-templated transcription, initiation Technology Type(s) cap analysis of gene expression Factor Type(s) Species • animal body part • cell type Sample Characteristic(s) Canis lupus familiaris • Rattus norvegicus • aortic smooth muscle cell • hepatocyte • mesenchymal stem cell

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Data Descriptor | Open Access | | Scientific Data

Design Type(s) species comparison design • organism part comparison design • transcription start site identification objective Measurement Type(s) DNA-templated transcription, initiation Technology Type(s) cap analysis of gene expression Factor Type(s) animal body part Sample Characteristic(s) Macaca mulatta • amygdala • caudate nucleus • cerebellum • globus pallidus • hippocampal formation • locus ceruleus • middle frontal gyrus • middle temporal gyrus • medulla oblongata • occipital gyrus • parietal lobe • putamen • spinal cord • substantia nigra • dorsal thalamus

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Data Descriptor | Open Access | | Scientific Data

Design Type(s) parallel group design • organism part comparison design Measurement Type(s) transcription profiling assay Technology Type(s) cap analysis of gene expression Factor Type(s) tissue Sample Characteristic(s) Homo sapiens • brain • heart • testis • retina • aortic smooth muscle cell • blood • lung • prostate gland • spleen • middle frontal gyrus • amygdala • hippocampal formation • thalamus • medulla oblongata • parietal lobe • substantia nigra • spinal cord • pineal body • globus pallidus • pituitary gland • occipital cortex • caudate nucleus • locus ceruleus • cerebellum • aortic endothelial cell • gingival fibroblast • CD14-positive monocyte • endothelial progenitor cell • aortic adventitial fibroblast • intestinal epithelial cell • mesothelium • annulus pulposus cell • stroma of pancreas • respiratory epithelial cell • mammary epithelial cell • placental epithelial cell • skeletal muscle cell • omentum preadipocyte • mast cell • renal cell carcinoma cell line • immortal human skin-derived cell line cell • maxillary sinus tumor cell line • immortal human uterine cervix-derived cell line cell • gastric signet ring cell adenocarcinoma • neurilemoma cell line • glioblastoma cell line • chronic myeloid leukemia cell line • acute lymphoblastic leukemia cell line • neuroblastoma cell line • cervical cancer cell line • osteosarcoma cell line • chondrosarcoma cell line • synovial sarcoma cell • myeloma cell line • lymphocytic leukemia cell line

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Data Descriptor | Open Access | | Scientific Data

Design Type(s) data integration objective • sequence data transformation objective Measurement Type(s) DNA-templated transcription, initiation Technology Type(s) sequence analysis data transformation Factor Type(s) Sample Characteristic(s) Homo sapiens • Mus musculus

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Data Descriptor | Open Access | | Scientific Data

Design Type(s) organism part comparison design • species comparison design • cell type comparison design • organism development design Measurement Type(s) DNA-templated transcription, initiation Technology Type(s) cap analysis of gene expression Factor Type(s) Species • Organism Part • life cycle stage • cell type Sample Characteristic(s) Mus musculus • Homo sapiens • cerebellum • visual cortex • ileum • Peyer's patch • stomach • axillary lymph node • aorta • substantia nigra • hippocampal formation • brain • heart • liver • meningeal cluster • bone marrow • spinal cord • raphe nuclei • corpus striatum • cortex • peripheral nervous system • kidney • neural system • hemolymphoid system • blood • spleen • mesoderm • hematopoietic system • ventral wall of dorsal aorta • placenta • ganglion • spiral organ of cochlea • small intestine • intestine • adrenal gland • eyeball of camera-type eye • pituitary gland • thymus • lung • female gonad • testis • bone tissue • diencephalon • muscle organ • medulla oblongata • forelimb • pancreas • gonad • corpora quadrigemina • skin of body • tongue • colon • caecum • vesicular gland • epididymis • amnion • mammary gland • uterus • submandibular gland • prostate gland • intestinal mucosa • urinary bladder • vagina • oviduct

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Data Descriptor | Open Access | | Scientific Data

Research & Analysis

Alistair Forrest, Piero Carninci and colleagues of the FANTOM Consortium provide a catalogue of human long non-coding RNA (lncRNA) genes and their expression profiles across samples from human primary cell types, tissues and cell lines. They used combined analyses of multiple data sets to identify 27,919 lncRNA genes with high-confidence 5′ ends, as well as a subset of 19,175 potentially functional lncRNA loci. The lncRNA catalogue and annotations are available through an open web resource.

Article | | Nature

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.

Letter | | Nature Genetics

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.

Analysis | | Nature Genetics

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.

Article | | Nature Genetics

FANTOM5 (standing for functional annotation of the mammalian genome 5) is the fifth major stage of a major international collaboration that aims to dissect the transcriptional regulatory networks that define every human cell type. Two Articles in this issue of Nature present some of the project's latest results. The first paper uses the FANTOM5 panel of tissue and primary cell samples to define an atlas of active, in vivo bidirectionally transcribed enhancers across the human body. These authors show that bidirectional capped RNAs are a signature feature of active enhancers and identify more than 40,000 enhancer candidates from over 800 human cell and tissue samples. The enhancer atlas is used to compare regulatory programs between different cell types and identify disease-associated regulatory SNPs, and will be a resource for studies on cell-type-specific enhancers. In the second paper, single-molecule sequencing is used to map human and mouse transcription start sites and their usage in a panel of distinct human and mouse primary cells, cell lines and tissues to produce the most comprehensive mammalian gene expression atlas to date. The data provide a plethora of insights into open reading frames and promoters across different cell types in addition to valuable annotation of mammalian cell-type-specific transcriptomes.

Article | | Nature

FANTOM5 (standing for functional annotation of the mammalian genome 5) is the fifth major stage of a major international collaboration that aims to dissect the transcriptional regulatory networks that define every human cell type. Two Articles in this issue of Nature present some of the project's latest results. The first paper uses the FANTOM5 panel of tissue and primary cell samples to define an atlas of active, in vivo bidirectionally transcribed enhancers across the human body. These authors show that bidirectional capped RNAs are a signature feature of active enhancers and identify more than 40,000 enhancer candidates from over 800 human cell and tissue samples. The enhancer atlas is used to compare regulatory programs between different cell types and identify disease-associated regulatory SNPs, and will be a resource for studies on cell-type-specific enhancers. In the second paper, single-molecule sequencing is used to map human and mouse transcription start sites and their usage in a panel of distinct human and mouse primary cells, cell lines and tissues to produce the most comprehensive mammalian gene expression atlas to date. The data provide a plethora of insights into open reading frames and promoters across different cell types in addition to valuable annotation of mammalian cell-type-specific transcriptomes.

Article | | Nature

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