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Resource:Functional Annotation of the Mammalian Genome

Name: Resource:Functional Annotation of the Mammalian Genome
Description: The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4.

FANTOM4
In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates.
In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome.

Tools
Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities.
EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities.

SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset.
Abbreviation: FANTOM
Parent Organization: Resource:RIKEN Brain Science Institute
Supporting Agency: King Abdullah University of Science and Technology, Max Planck Society for the Advancement of Science, SA National Bioinformatics Network, Claude Leon Foundation, National Health and Medical Research Council, Scuola Interpolitecnica di Dottorato, NIMH
Grant: MH062261
Resource Type(s): Database, Software resource
Resource: Resource
URL: http://fantom.gsc.riken.jp
*Id: nif-0000-30552
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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Facts about Resource:Functional Annotation of the Mammalian GenomeRDF feed
AbbrevFANTOM  +
CurationStatusuncurated  +
DefiningCitationhttp://fantom.gsc.riken.jp  +
DefinitionThe FANTOM consortium is an international The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4.

FANTOM4
In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates.
In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome.

Tools
Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities.
EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities.

SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset.
carry out MARA on your own dataset.
GrantCategory:MH062261   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, and Software resource  +
Idnif-0000-30552  +
Is part ofResource:RIKEN Brain Science Institute  +
LabelResource:Functional Annotation of the Mammalian Genome  +
ModifiedDate18 July 2014  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
Supporting AgencyKing Abdullah University of Science and Technology  +, Max Planck Society for the Advancement of Science  +, SA National Bioinformatics Network  +, Claude Leon Foundation  +, Resource:PhenoGO  +, Scuola Interpolitecnica di Dottorato  +, and National Institute of Mental Health  +