Cargando…

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbat...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kawaji, Hideya, Severin, Jessica, Lizio, Marina, Waterhouse, Andrew, Katayama, Shintaro, Irvine, Katharine M, Hume, David A, Forrest, Alistair RR, Suzuki, Harukazu, Carninci, Piero, Hayashizaki, Yoshihide, Daub, Carsten O
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2009
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688931/ https://www.ncbi.nlm.nih.gov/pubmed/19374775 http://dx.doi.org/10.1186/gb-2009-10-4-r40

Ejemplares similares

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
por: Kawaji, Hideya, et al.
Publicado: (2011)

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types
por: Kawaji, Hideya, et al.
Publicado: (2017)

Beyond the FANTOM4
por: Suzuki, Harukazu, et al.
Publicado: (2010)

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
por: Severin, Jessica, et al.
Publicado: (2009)

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki
por: Abugessaisa, Imad, et al.
Publicado: (2016)

Linking FANTOM5 CAGE peaks to annotations with CAGEscan
por: Bertin, Nicolas, et al.
Publicado: (2017)

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium
por: Yu, Nancy Yiu-Lin, et al.
Publicado: (2015)

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
por: Lizio, Marina, et al.
Publicado: (2019)

Gateways to the FANTOM5 promoter level mammalian expression atlas
por: Lizio, Marina, et al.
Publicado: (2015)

Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome
por: Hayashizaki, Yoshihide, et al.
Publicado: (2006)

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
por: Lizio, Marina, et al.
Publicado: (2015)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals
por: Lizio, Marina, et al.
Publicado: (2017)

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
por: Abugessaisa, Imad, et al.
Publicado: (2017)

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
por: Rye, Morten, et al.
Publicado: (2014)

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes
por: Kawaji, Hideya, et al.
Publicado: (2009)

Hidden layers of human small RNAs
por: Kawaji, Hideya, et al.
Publicado: (2008)

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
por: Kawaji, Hideya, et al.
Publicado: (2006)

Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer
por: Itoh, Masayoshi, et al.
Publicado: (2012)

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli
por: Vacca, Annalaura, et al.
Publicado: (2018)

Dynamic usage of transcription start sites within core promoters
por: Kawaji, Hideya, et al.
Publicado: (2006)

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs
por: Abugessaisa, Imad, et al.
Publicado: (2020)

Monitoring transcription initiation activities in rat and dog
por: Lizio, Marina, et al.
Publicado: (2017)

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
por: Vitezic, Morana, et al.
Publicado: (2010)

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage
por: Carbajo, Daniel, et al.
Publicado: (2015)

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses
por: Haberle, Vanja, et al.
Publicado: (2015)

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells
por: Mina, Marco, et al.
Publicado: (2015)

Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
por: Maeda, Norihiro, et al.
Publicado: (2006)

Correction to: Relatively frequent switching of transcription start sites during cerebellar development
por: Zhang, Peter, et al.
Publicado: (2018)

Paradigm shifts in genomics through the FANTOM projects
por: de Hoon, Michiel, et al.
Publicado: (2015)

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes
por: Qin, Xian-Yang, et al.
Publicado: (2017)

MOIRAI: a compact workflow system for CAGE analysis
por: Hasegawa, Akira, et al.
Publicado: (2014)

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation
por: Tomaru, Yasuhiro, et al.
Publicado: (2014)

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
por: Kawaji, Hideya, et al.
Publicado: (2014)

Alternate transcription of the Toll-like receptor signaling cascade
por: Wells, Christine A, et al.
Publicado: (2006)

Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis
por: Horie, Masafumi, et al.
Publicado: (2016)

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution
por: Ehrlund, Anna, et al.
Publicado: (2017)

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease
por: Baillie, J. Kenneth, et al.
Publicado: (2017)

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β
por: Alhendi, Ahmad M. N., et al.
Publicado: (2018)

CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts
por: Katayama, Shintaro, et al.
Publicado: (2007)

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages
por: Roy, Sugata, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_134gdp69605t1fdej3q0fm0on6