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fantom2.gsc.riken.jp

FANTOM

Go to current FANTOM site. FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone. It provides not simply the gene functions themselves, but also many other informative and useful data describing functional information about the clones. Release of FANTOM DB 2.1.1 (August 31st, 2004). Release of FANTOM DB 2.0 and 2.1 (December 5th, 2002). The outcome of FANTOM2 collaborative research was published on Nature. (December 5th, 2002). Annoucement of FANTOM2 MATRICS (December 29th, 2001).

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FANTOM | fantom2.gsc.riken.jp Reviews
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Go to current FANTOM site. FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone. It provides not simply the gene functions themselves, but also many other informative and useful data describing functional information about the clones. Release of FANTOM DB 2.1.1 (August 31st, 2004). Release of FANTOM DB 2.0 and 2.1 (December 5th, 2002). The outcome of FANTOM2 collaborative research was published on Nature. (December 5th, 2002). Annoucement of FANTOM2 MATRICS (December 29th, 2001).
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1 fantom database
2 download site
3 copyright notice
4 fantom3
5 fantom current
6 riken ger lab
7 riken gsc
8 riken
9 announcements
10 history
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FANTOM | fantom2.gsc.riken.jp Reviews

https://fantom2.gsc.riken.jp

Go to current FANTOM site. FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone. It provides not simply the gene functions themselves, but also many other informative and useful data describing functional information about the clones. Release of FANTOM DB 2.1.1 (August 31st, 2004). Release of FANTOM DB 2.0 and 2.1 (December 5th, 2002). The outcome of FANTOM2 collaborative research was published on Nature. (December 5th, 2002). Annoucement of FANTOM2 MATRICS (December 29th, 2001).

INTERNAL PAGES

fantom2.gsc.riken.jp fantom2.gsc.riken.jp
1

Menu page

http://fantom2.gsc.riken.jp/db

How to refer to the FANTOM DB. Contact persons: fantom-help@gsc.riken.go.jp. RIKEN (The Institute of Physical and Chemical Research) / NTT Software Corporation.

2

FANTOM

http://fantom2.gsc.riken.jp/fantom2/doc/announce/fantom2release.html

Release of the largest-scale mouse transcriptome data which contribute to progress of gene discoveries. It is difficult to predict all genes from from the genomic sequence data alone. Substantial transcript data is necessary to identify all genes. The major findings of this research are as follows:. The collection of the largest and high-quality set of full-length cDNA clones and sequences. Highly quality functional annotation. Integrated data of the mouse genome and the transcriptome.

3

FANTOM

http://fantom2.gsc.riken.jp/fantom2/doc/reference.html

To cite resources available from the FANTOM web site in your publications, use a following format. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I and II Team. The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection. Map of RIKEN clones on Human Genome and Mouse Chromosomes.

4

information

http://fantom2.gsc.riken.jp/doc/information.html

Information related to FANTOM data. Supplementary Table 5A in Nature 409:685-690, 2001. Detailed post-FANTOM meeting analysis of sequences containing motifs MD00121,. MD00129, MD00137 and MD00139 revealed that the DECODER predicted ORFs. Including the motif regions overlap with B2, B1 intracisternal A-particle LTR,. And mammalian apparent LTR-retrotransposon repeat elements, respectively. The. Four motifs are therefore false positives and the sequences constitute.

5

FANTOM

http://fantom2.gsc.riken.jp/fantom2/doc/history.html

The RIKEN Mouse Gene Encyclopedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We, the RIKEN Genome Exploration Research (GER) group, have organized an international meeting (FANTOM) in 2000 to annotate our first 21,076 cDNAs. The outcome was published in Nature vol.409, page 685-690. 1 FANTOM2 Typhoon Meeting. After the ...

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hackingisbelieving.org hackingisbelieving.org

CV - Hacking is believing

http://www.hackingisbelieving.org/cv

Advanced Center for Computing and Communication, Japan. Ruby, R/Bioconductor, Matlab, C , Python. Data analysis of Next generation sequencer, (ChIP-seq, RNA-seq). Statistics, Machine learning. A parser for files of GPS (Genome Positioning System). In Ruby, RubyGems). R package for quantitative comparison of differential. Meta-analysis of RNA-Seq count data in. Multiple studies (working with Mr. Koki. Biological Database and API. Full-text search in NCBI RefSeq and/or UniProt-KB on R. Source Forge ( itoshi.

bit.riken.jp bit.riken.jp

Software & Database | Bioinformatics Research Unit

http://bit.riken.jp/software

RIKEN Advanced Center for Computing and Communication. Software & Database. Contact & Access. RIKEN Bioinformatics Seminar Series. Software & Database. SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Linux distribution for Bioinformatics Analysis. A parser for files of GPS (Genome Positioning System). In Ruby, RubyGems. R package for quantitative comparison of differential ChIP-seq data. Meta-analysis of RNA-Seq count data in.

fantom3.gsc.riken.jp fantom3.gsc.riken.jp

FANTOM3::Related Database

http://fantom3.gsc.riken.jp/related_db.html

Protein Protein Interaction Viewer). Expression-based Imprint Candidate Organiser). READ (RIKEN Expression Array Database). NCBI (National Center for Biotechnology Information). EBI (European Bioinformatics Institute). DDBJ (DNA Data Bank of Japan). MGA (Mass sequence for Genome Annotation) (CAGE data download). PDB (Protein Data Bank). MGI (Mouse Genome Informatics). KEGG (Kyoto Encyclopedia of Genes and Genomes). GO (the Gene Ontology). ExPASy (Expert Protein Analysis System) Proteomics Server.

fantom3.gsc.riken.jp fantom3.gsc.riken.jp

FANTOM3::FAQ

http://fantom3.gsc.riken.jp/FAQ.html

Where can I get a list of non-coding cDNAs? Please find here, ftp:/ fantom.gsc.riken.jp/FANTOM3/noncoding/. Where can I get the transcribed genome regions defined by 5' and 3' ends? Please find here, ftp:/ fantom.gsc.riken.jp/FANTOM3/boundary set/. Where can I get the GIS and GSC sequences? Please find here, ftp:/ fantom.gsc.riken.jp/FANTOM3/GIS/. And/or ftp:/ fantom.gsc.riken.jp/FANTOM3/GSC/. Where can I get the 5,154 new protein sequences? Where can I find promoters determined by CAGE? We classified CA...

fantom3.gsc.riken.jp fantom3.gsc.riken.jp

FANTOM3::Related papers

http://fantom3.gsc.riken.jp/related_ref.html

Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Ajioka I, Maeda T, Nakajima K. Keio J Med. 2006 Sep;55(3):107-10. Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Kiyosawa H, Mise N, Iwase S, Hayashizaki Y, Abe K. Genome Res. 2005 Apr;15(4):463-74. Epub 2005 Mar 21. Development of a spot reliability evaluation score for DNA microarrays. Construction of representative tr...

fantom3.gsc.riken.jp fantom3.gsc.riken.jp

FANTOM3::FANTOM3 papers

http://fantom3.gsc.riken.jp/f3papers.html

Two milestone papers in the special issue: "Mapping RNA Form and Function". The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63. Antisense transcription in the mammalian transcriptome. Science. 2005 Sep 2;309(5740):1564-6. Another milestone paper in Nature Genetics. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006 Jun;38(6):626-635. The Genome Network/FANTOM3 article collection. Hayashizaki Y, Carninci P. Differential use of s...

fantom.gsc.riken.jp fantom.gsc.riken.jp

FANTOM3::Databases

http://fantom.gsc.riken.jp/3

Go to current FANTOM site. All data and resources used in this project are available to the community from this page. Please see also the press release text. For a more extensive summary of the project, and the databases below. Notice] FANTOM servers, including the cDNA viewer and the CAGE databases, will stop on 22nd October, 2007 (JST). Are published in the Genome Network/FANTOM3 article collection. Another milestone paper is published. Its supplementary information is avaliable from here.

fantom3.gsc.riken.jp fantom3.gsc.riken.jp

FANTOM3::Photos

http://fantom3.gsc.riken.jp/photos.html

Welcome to the FANTOM3 photo gallery! Please click the pictures to enlarge. Tanabata Meeting : July 05 - 08, RIKEN, GSC, Japan. Harvest Meeting : September 10 - 15, RIKEN, Japan. Genome Exploration Research Group. RIKEN Genomic Sciences Center(GSC).

fantom3.gsc.riken.jp fantom3.gsc.riken.jp

FANTOM3::History

http://fantom3.gsc.riken.jp/history.html

FANTOM is the abbreviation of the "Functional Annotation of the Mouse", or the "Functional Annotation of the Mammalians", as we have produced data to analyze the human transcriptome. The objectives of our research activities have been implemented in the last few years with support of the FANTOM International Consortium organized and led by RIKEN (The Institute of Physical and Chemical Research), and in the recent year, with the support of the Genome Network Project. Genome Research special issue June 2003.

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FANTOM

Go to current FANTOM site. FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone. It provides not simply the gene functions themselves, but also many other informative and useful data describing functional information about the clones. Release of FANTOM DB 2.1.1 (August 31st, 2004). Release of FANTOM DB 2.0 and 2.1 (December 5th, 2002). The outcome of FANTOM2 collaborative research was published on Nature. (December 5th, 2002). Annoucement of FANTOM2 MATRICS (December 29th, 2001).

fantom2.gsc.riken.jp fantom2.gsc.riken.jp

FANTOM

Go to current FANTOM site. FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone. It provides not simply the gene functions themselves, but also many other informative and useful data describing functional information about the clones. Release of FANTOM DB 2.1.1 (August 31st, 2004). Release of FANTOM DB 2.0 and 2.1 (December 5th, 2002). The outcome of FANTOM2 collaborative research was published on Nature. (December 5th, 2002). Annoucement of FANTOM2 MATRICS (December 29th, 2001).

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