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FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones

H. Bono
2002 Nucleic Acids Research  
FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis  ...  FANTOM DB thus provides curated functional annotation to RIKEN full-length enriched mouse clones, and has links to other public resources.  ...  ACKNOWLEDGEMENTS We acknowledge all the members of the FANTOM consortium for the use of FANTOM annotation. We also acknowledge Dr M. Brownstein for comments and editing the manuscript.  ... 
doi:10.1093/nar/30.1.116 pmid:11752270 pmcid:PMC99137 fatcat:dmms4qodt5b53blx3rbfzchufy

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  
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  ...  In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced.  ...  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

Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs

Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G. Engström, Boris Lenhard, Rajith N. Aturaliya, Serge Batalov, Kirk W. Beisel, Carol J. Bult, Colin F. Fletcher (+22 others)
2006 PLoS Genetics  
T he international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs  ...  Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and  ...  Acknowledgments We thank all annotators for their contribution to functional annotation, especially Yumi Onodera for her exceptional contribution. Funding.  ... 
doi:10.1371/journal.pgen.0020062 pmid:16683036 pmcid:PMC1449903 fatcat:seovzd67xffxzlr3xuu7dalyna

Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set

L. M. Schriml
2003 Genome Research  
HG00330 for the Mouse Genome Database.  ...  The content of this publication does not necessarily reflect the views or policies of the U.S.  ...  Here we identify mouse cDNA sequences in the FANTOM2 data set for a set of 67 human disease genes that as of May 2002 had no corresponding mouse cDNA annotated in the Mouse Genome Informatics (MGI) database  ... 
doi:10.1101/gr.979503 pmid:12819148 pmcid:PMC403698 fatcat:vp6lx5pqcfcvpcmzq43zxs2wzm

Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS

T. Nagashima
2003 Genome Research  
Using FACTS, we found that 47.5% of the 60,770 RIKEN mouse cDNA FANTOM2 clone annotations were informative for text searches.  ...  FACTS (Functional Association/Annotation of cDNA Clones from Text/Sequence Sources) is a semiautomated knowledge discovery and annotation system that integrates molecular function information derived from  ...  ACKNOWLEDGMENTS We thank Mihaela Zavolan for discussions and for providing the accessions of the variant and nonvariant clusters of MouSDB.  ... 
doi:10.1101/gr.1019903 pmid:12819151 pmcid:PMC403704 fatcat:erzymgcaq5cihazysmmaoblwom

RNAdb 2.0--an expanded database of mammalian non-coding RNAs

K. C. Pang, S. Stephen, M. E. Dinger, P. G. Engstrom, B. Lenhard, J. S. Mattick
2007 Nucleic Acids Research  
function.  ...  RNAdb is a comprehensive database of mammalian non-protein-coding RNAs (ncRNAs).  ...  ACKNOWLEDGEMENTS The authors would like to thank Martin Frith and Jinfeng Liu for assistance with annotation of the FANTOM3 ncRNAs, Evgeny Nudler for providing HSR-1 sequences, Jhumku Kohtz for providing  ... 
doi:10.1093/nar/gkl926 pmid:17145715 pmcid:PMC1751534 fatcat:wvjwc3r3zjb7toydvoeg6w5l5i

Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation

H. Kiyosawa
2003 Genome Research  
We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional  ...  4 Present address: RIKEN Tsukuba Institute,  ...  This study was supported by a Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to Y.H.  ... 
doi:10.1101/gr.982903 pmid:12819130 pmcid:PMC403655 fatcat:s33wlealdfbarck5j7zu2eq5b4

Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection

K. Numata
2003 Genome Research  
In this situation, the RIKEN mouse full-length cDNA collection, called FANTOM2 clone set (Okazaki et al. 2002) , provides the largest available resource in any mammal for the discovery of candidate functional  ...  This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences, by using a systematic computational filtering  ... 
doi:10.1101/gr.1011603 pmid:12819127 pmcid:PMC403720 fatcat:qxzapgbpbvhgtgaqxkp7typiti

Identification and analysis of novel genes expressed in the mouse embryonic facial primordia

Jennifer, S. Bennetts
2006 Frontiers in Bioscience  
Cloning of epitope-tagged coding sequences for candidate genes 3.4. Cell culture and immunofluorescence 4. Results 4.1.  ...  Cloning into expression vectors and transfection into mammalian cells 5. Discussion 5.1.  ...  Cloning of epitope-tagged coding sequences for candidate genes Where available, RIKEN clones containing fulllength predicted coding sequences (supplied from the RIKEN mouse cDNA clone set FANTOM I and  ... 
doi:10.2741/1997 pmid:16720340 fatcat:ukaccqrasvf5fmizlwtx4hi2rq

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

Keiichi Mochida, Yukiko Uehara-Yamaguchi, Fuminori Takahashi, Takuhiro Yoshida, Tetsuya Sakurai, Kazuo Shinozaki, Qiong Wu
2013 PLoS ONE  
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes.  ...  Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA  ...  Acknowledgments The authors thank Yoshihiko Onda and Tadamasa Sasaki of RIKEN Center for Sustainable Resource Science for their valuable suggestions and comments on the manuscript and database.  ... 
doi:10.1371/journal.pone.0075265 pmid:24130698 pmcid:PMC3793998 fatcat:xw3jbyk5vnhftamqldsi6taar4

Genetic control of the innate immune response

Christine A Wells, Timothy Ravasi, Geoffrey J Faulkner, Piero Carninci, Yasushi Okazaki, Yoshihide Hayashizaki, Matthew Sweet, Brandon J Wainwright, David A Hume
2003 BMC Immunology  
The mouse strains examined varied greatly in the number, amplitude and rate of induction of genes expressed in response to LPS.  ...  This study examines the influence of genetic background on host-pathogen interactions, by assessing the transcriptional responses of macrophages from five inbred mouse strains to lipopolysaccharide (LPS  ...  Analysis of data was performed on software and computing hardware provided by the SRC for Functional and Applied Genomics, The University of QLD.  ... 
doi:10.1186/1471-2172-4-5 pmid:12826024 pmcid:PMC194878 fatcat:e4dkyzcubvhcdlm242g4wkmb2u

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

Hiromasa Ono, Osamu Ogasawara, Kosaku Okubo, Hidemasa Bono
2017 Scientific Data  
Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes.  ...  Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required.  ...  Thus, a user can download a concatenated version of all the data at the RefEx website, including the sequences, the functional annotation of the cDNA clones, and the logtransformed ratios of the gene expression  ... 
doi:10.1038/sdata.2017.105 pmid:28850115 pmcid:PMC5574374 fatcat:hl4qdkkhpbac3jvowvvretbyn4

The Comparative Proteomics of Ubiquitination in Mouse

C. A.M. Semple
2003 Genome Research  
It also benefited from many discussions with other FANTOM Consortium members and the hospitality of the RIKEN Genomic Sciences Center.  ...  Colin Gordon read an earlier version of the manuscript, and an anonymous reviewer provided useful comments.  ...  mouse transcriptome (The FANTOM Consortium and the RIKEN GER Group Phase I and II Team 2002).  ... 
doi:10.1101/gr.980303 pmid:12819137 pmcid:PMC403670 fatcat:4d7ai65qifgrfl7zexzvypsayy

A high-throughput screening of genes that encode proteins transported into the endoplasmic reticulum in mammalian cells

T. Ozawa
2005 Nucleic Acids Research  
The compartments of eukaryotic cells maintain a distinct protein composition to perform a variety of specialized functions.  ...  Complementary DNA (cDNA) libraries fused to the N-terminal halves of DnaE and EGFP are introduced in mammalian cells with retroviruses.  ...  . gov/BLAST/) and FANTOM database (http://fantom2.gsc.  ... 
doi:10.1093/nar/gni032 pmid:15731327 pmcid:PMC549573 fatcat:7xcty6ynjnhkjk4cztinqd45he

Screening for candidate genes involved in the production of mouse subventricular zone proliferative cells and an estimation of their changes in evolutionary pressure during primate evolution

Hidenori Tabata, Tsuyoshi Hachiya, Koh-ichi Nagata, Yasubumi Sakakibara, Kazunori Nakajima
2013 Frontiers in Neuroanatomy  
The dramatic increase in the number of bRGs in primates, especially in humans, is thought to underlie the acquisition of a huge cortex during evolution.  ...  These genes were considered to be among the candidates responsible for the regulation of the REP/SEP production rate.  ...  of Education, Culture, Sports, and Science and Technology of Japan, Keio Gijuku Academic Development Funds, and Keio University Special Grant-in-Aid for Innovative Collaborative Research Projects.  ... 
doi:10.3389/fnana.2013.00024 pmid:23914158 pmcid:PMC3728626 fatcat:uq2wowv56zfpnnji2eugaz26nq
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