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Protocols

FANTOM specifications

Information


Unique identifier OMICS_18179
Name FANTOM
Alternative names Functional ANnoTation Of the Mammalian genome, FANTOM5 SSTAR, SSTAR
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 6.0
Content license Other
Maintained Yes

Maintainer


  • person_outline Alistair RR Forrest

Publications for Functional ANnoTation Of the Mammalian genome

FANTOM citations

 (229)
library_books

NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

2018
Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] as described above. Regions displaying altered chromatin accessibility were mapped to genomic annotations or repeat regions using bedtools v2.26.0. For the genomic annotations, we used TSSs from the FANTOM database, repeats from repeatMasker (UCSC genome browser) and other genomic features (exons, introns, UTRs, etc.) were extracted from the UCSC Table Browser. The enhancers were identified based […]

library_books

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

2018
Nat Commun
PMCID: 5916929
PMID: 29695774
DOI: 10.1038/s41467-018-03766-z

[…] ing at least two tags in at least eight samples (Supplementary Fig. ). Ten technical replicate libraries were included at this stage, but discarded in final expression measurement table. Overlap with FANTOM5 enhancers (http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/) was calculated using the intersectbed command from BEDTools package. […]

library_books

Opportunities and obstacles for deep learning in biology and medicine

2018
PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] ach of the remaining datasets and achieved results close to the model trained on all 164 datasets together. In another example, Min et al. [] demonstrated how training on the experimentally validated FANTOM5 permissive enhancer dataset followed by fine-tuning on ENCODE enhancer datasets improved cell-type-specific predictions, outperforming state-of-the-art results. In drug design, general RNN mod […]

library_books

Genomic Analysis of a Pan Resistant Isolate of Klebsiella pneumoniae, USA 2016

2018
MBio
PMCID: 5885025
PMID: 29615503
DOI: 10.1128/mBio.00440-18

[…] to the polished long-read contigs for minor error correction using Pilon 1.21 (). Acquired antimicrobial resistance genes were identified on high-quality contigs using the Resfinder repository () and SSTAR V1.1.01 (). Finally, additional genes were detected with PGAP () and ISfinder () to identify genes contributing to displayed phenotypic resistance which could not be explained by acquired mechan […]

call_split

Phenotypic and Genotypic Characterization of Enterobacteriaceae Producing Oxacillinase 48–Like Carbapenemases, USA

2018
PMCID: 5875285
PMID: 29553324
DOI: 10.3201/eid2404.171377
call_split See protocol

[…] lele sequences (http://www.pubmlst.org) by using SRST2 software (Illumina) (). We described antimicrobial resistance genotype profiles from assembled Illumina and Pacific Biosciences contigs by using SSTAR V1.0 () in combination with the ARG-ANNOT () and ResFinder () repositories.We used the PlasmidFinder database (http://www.genomicepidemiology.org/) to detect plasmid replicon sequences among Ill […]

call_split

Long Non Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue

2018
PMCID: 5952343
PMID: 29580841
DOI: 10.1016/j.ebiom.2018.03.010
call_split See protocol

[…] e transcript abundance quantification was first conducted using the ultrafast quasi-alignment tool Kallisto (), which pseudo-aligned the sequencing reads from each sample to the assembly based on the FANTOM-CAT. Then the gene-level estimates, representing the overall transcriptional output of each gene, were obtained by summing the corresponding transcript-level estimates using a Bioconductor pack […]

Citations

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FANTOM institution(s)
RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan
FANTOM funding source(s)
Supported by research grants to RIKEN Center for Life Science Technologies, RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Integrative Medical Sciences from the Japan Ministry of Education, Culture, Sports, Science and Technology (MEXT); Japan Society for the Promotion of Science KAKENHI Grants [16H02902, 16K12529]; Research grant from National Bioscience Database Center of the Japan Science and Technology Agency.

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