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Integrated analysis of the genome and the transcriptome by FANTOM

S. Katayama
2004 Briefings in Bioinformatics  
Kasukawa for valuable advice and to K. Yoshida for providing us with the samples. We gratefully acknowledge helpful discussions with J. Adachi on several points about ProCrest.  ...  CONCLUSION: BEYOND FANTOM Integrated analysis of the genome and the transcriptome creates a synergistic effect, providing extremely valuable insights into the nature of life.  ...  However, the integration of the genome and the transcriptome should be the basis of all analyses, including dynamic analyses.  ... 
doi:10.1093/bib/5.3.249 pmid:15383211 fatcat:hg5423zssrbbdmc3qfihlmluxu

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa (+1 others)
2018 Nucleic Acids Research  
We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive  ...  It contains the most complete and comprehensive sets of actively transcribed enhancers and promoters in the human and mouse genomes.  ...  ACKNOWLEDGMENTS The authors would like to thank Dr A.R.R. Forrest for scientific coordination of the FANTOM5 collaboration, Dr C. Plessy for helping the manuscript preparation, J. Harsh-  ... 
doi:10.1093/nar/gky1099 pmid:30407557 pmcid:PMC6323950 fatcat:xc6iffwzbngsdcqsrm7aptzgxa

Special FANTOM2 Issue

Y. Hayashizaki
2003 Genome Research  
Integrated analysis of the genome and transcriptome created a synergistic effect, providing extremely valuable insights into the nature of life.  ...  In this issue, we present papers on FANTOM activity, describing analyses based on the first data for the genome and transcriptome.  ... 
doi:10.1101/gr.1400103 fatcat:uzptwa6n3jd5joq25fsm4ismpi

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

H. Kawaji, J. Severin, M. Lizio, A. R. R. Forrest, E. van Nimwegen, M. Rehli, K. Schroder, K. Irvine, H. Suzuki, P. Carninci, Y. Hayashizaki, C. O. Daub
2010 Nucleic Acids Research  
to uncover novel components of the transcriptome employing a series of highthroughput experiments.  ...  effects of regulation by transcription factors.  ...  ACKNOWLEDGEMENTS We would like to thank all of the members in the FANTOM consortium for fruitful collaboration.  ... 
doi:10.1093/nar/gkq1112 pmid:21075797 pmcid:PMC3013704 fatcat:wcrbnmvr4zd3heyaqgo4wvznpu

Beyond the FANTOM4

Harukazu Suzuki, Piero Carninci, Carsten Daub, Jun Kawai, Yoshihide Hayashizaki
2010 Genome Biology  
RIKEN OSC has a long history of transcriptome analysis using DNA sequencers; we also organize the international consortium Functional Annotation of Mammalian Genome (FANTOM; Figure 1) .  ...  The deepCAGE data were also used to analyze the promoter activity of repeat elements and to discover new small RNA (tiRNA) by integration with the small RNA sequencing.  ... 
doi:10.1186/gb-2010-11-s1-o11 fatcat:76wa7q6dzzhohcrwszouoy3acm

Paradigm shifts in genomics through the FANTOM projects

Michiel de Hoon, Jay W. Shin, Piero Carninci
2015 Mammalian Genome  
The FANTOM Consortium has provided the most comprehensive mouse cDNA collection for functional studies and extensive maps of the human and mouse transcriptome comprising promoters, enhancers, as well as  ...  and, more recently, expression profiling at single-nucleotide resolution by cap-analysis gene expression.  ...  Acknowledgments We are indebted with all the members of the FANTOM consortium and RIKEN colleagues, in particular at RIKEN Center for Life Science Technologies and RIKEN PMI.  ... 
doi:10.1007/s00335-015-9593-8 pmid:26253466 pmcid:PMC4602071 fatcat:7y5if7dg7fao3pp6wogpducl2y

READ: Practical Analysis System of Mouse Transcriptome with the FANTOM Database

Hidemasa Bono, Takeya Kasukawa, Itoshi Nikaido, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki
2001 Genome Informatics Series  
Acknowledgements This study has been supported by Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese  ...  Government and ACT-JST (Research and Development for Applying Advanced Computational Science and Technology) of Japan Science and Technology Corporation (JST).  ...  Currently it can be queried not only by the RIKEN cDNA clone identifier on the chip and by keywords in the database description, but also by the log-transformed ratio of gene expression intensity in all  ... 
doi:10.11234/gi1990.12.232 fatcat:ahmff4uahrdoxhsmrvha5fdhxq

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

Hideya Kawaji, Takeya Kasukawa, Alistair Forrest, Piero Carninci, Yoshihide Hayashizaki
2017 Scientific Data  
With the full-length cDNA technology developed at RIKEN 1 , the first, second and third rounds of the FANTOM projects surveyed the mammalian transcriptome landscape by sequencing a large collection of  ...  The latest project from the FANTOM consortium, an international collaborative effort initiated by RIKEN, generated atlases of transcriptomes, in particular promoters, transcribed enhancers, and long-noncoding  ...  With the full-length cDNA technology developed at RIKEN 1 , the first, second and third rounds of the FANTOM projects surveyed the mammalian transcriptome landscape by sequencing a large collection of  ... 
doi:10.1038/sdata.2017.113 pmid:28850107 pmcid:PMC5574373 fatcat:5ooytyc2lndm3gvkx4kv6atvgy

Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome

Yoshihide Hayashizaki, Piero Carninci
2006 PLoS Genetics  
Citation: Hayashizaki Y, Carninci P (2006) Genome network and FANTOM3: Assessing the complexity of the transcriptome. PLoS Genet 2(4): e63.  ...  Acknowledgments We would like to thank Nabiko Suzuki, Miki Nishikawa, Hiroko Himei, and Yukari Shigemoto for secretarial assistance, Ann Karlsson for scientific English editing, and  ...  About the FANTOM and Genome Network Collaboration FANTOM and GN (originally a Japanese national project for establishing a system for connecting genes with phenotypes and drug targets/effects by using  ... 
doi:10.1371/journal.pgen.0020063 pmid:16683037 pmcid:PMC1449904 fatcat:37jpnpun7ndnzjyuh64vflqwme

Discovery of the "RNA continent" through a contrarian's research strategy

Yoshihide Hayashizaki
2011 Genes & Genetic Systems  
These two genome projects established that the number of letters in the genome, which is the blueprint of life, is finite, that the number of RNA molecules derived from it is also finite, and that the  ...  Led by our research group at RIKEN, it was a full-length cDNA project which aimed to decode the whole RNA (transcriptome) using the mouse as a model.  ...  The following FANTOM 3 saw the development of two new transcriptome analysis tools, the Cap Analysis of Gene Expression (CAGE) method and the Gene Signature Cloning (GSC) method, which can identify transcription  ... 
doi:10.1266/ggs.86.221 pmid:22214591 fatcat:qv3uuuolu5gs7e37emsxye56qa

Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome

H. Bono
2003 Genome Research  
The mouse metabolome confirmed by cDNA analysis includes almost all of the enzymes of well known pathways such as the tricarboxylic acid cycle and urea cycle.  ...  The information derived from coexpression from the cDNA microarray analysis of enzymes of known function may lead to identification of the missing components of the metabolome, and will add new insights  ...  This study was supported by a Research Grant for the RIKEN Genome Exploration Re-search Project, and by a Grant-in-Aid for Scientific Research on Priority Areas (C) "Genome Information Science," both from  ... 
doi:10.1101/gr.974603 pmid:12819132 pmcid:PMC403659 fatcat:klisrniorvbwvbvalf6roafekq

Transcriptomics resources of human tissues and organs

M. Uhlen, B. M. Hallstro m, C. Lindskog, A. Mardinoglu, F. Ponten, J. Nielsen
2016 Molecular Systems Biology  
Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome-wide transcriptome analyses of different tissues.  ...  Moreover, we discuss the applications of publicly available omics data for building genome-scale metabolic models, used for analyzing cell and tissue functions both in physiological and in disease contexts  ...  Funding was provided by the Knut and Alice Wallenberg Foundation. Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.15252/msb.20155865 pmid:27044256 pmcid:PMC4848759 fatcat:i5gdtdc7zjgp7nbwnnifowzcta

Functional Annotation of RIKEN Mouse cDNA Clones Using GNF Expression Atlas

S. Batalov
2003 Genome Research  
Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. 99: 4465-4470.  ...  REFERENCES The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I and Phase II Team. 2002.  ... 
doi:10.1101/gr.1457103 fatcat:wrwhd3w6frdtpniuciknyp5uwm

Data resources for human functional genomics

Kristin G. Ardlie, Roderic Guigó
2017 Current Opinion in Systems Biology  
interrogate both the coding and the noncoding genome, to decipher the rules by which genes and gene networks are regulated, and to be able to predict the molecular, cellular, and ultimately organismal  ...  One of the most pressing needs in medical and evolutionary genomes is characterizing and interpreting the function of the millions of genetic variants in the human genome, most of which are rare, and many  ...  FANTOM pioneered the high throughput use of Cap Analysis of Gene Expression (CAGE) analysis.  ... 
doi:10.1016/j.coisb.2016.12.019 pmid:28989986 pmcid:PMC5625631 fatcat:4767mb5b5bhgbhctuartvgt23i

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs (+13 others)
2016 Nucleic Acids Research  
In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced.  ...  Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FAN-TOM  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the members in the FANTOM consortium for fruitful collaboration.  ... 
doi:10.1093/nar/gkw995 pmid:27794045 pmcid:PMC5210666 fatcat:5z6fqqnewbbi7a5mwaipsgmi44
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