FANTOM DB 1.1 release Notes
October 4th, 2001

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Introduction

The FANTOM DB consists of of functional annotations for the RIKEN full-length
cDNA clones. It provides not simply the gene functions themselves, but also many
other informative and useful data describing functional information about the clones. 
See FANTOM introduction at FANTOM DB web site 
(http://fantom.gsc.riken.go.jp/doc/introduction.html). 

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FANTOM DB 1.1 (released on October 4th, 2001) 
1. The clone set and sequences. 
The clone set for FANTOM DB 1.1 contains 21,076 RIKEN cDNA clones which were 
prepared for FANTOM DB 1.0 (released on February 8th, 2001). See FANTOM1.1 ID
table at FANTOM DB web site 
(http://fantom.gsc.riken.go.jp/doc/idtable1-1.txt). 

ID difference between FANTOM DB1.1 and FANTOM DB1.0 (February 8th, 2001) 
Clone ID: Same for all
Seqid:Seqids for 120 clones were changed. 
Among these 120 clones, 
Both sequence qualities and sequences were changed for 24 clones. 
Sequence qualities were changed but sequences were not changed for 96 clones. 


2. Annotation updated

2.1. Annotation updated based on SPTR(SWISS-PROT + TrEMBL) data and Pfam
Previous FANTOM data (FANTOM DB1.0) were annotated mainly based on analyzed
results between FANTOM sequences and public dababase of amino acids or DNA
sequences in August, 2000. For FANTOM DB1.1, we did FASTY and BLASTX search
between FANTOM DB1.1 sequences and SPTR (SWISS-PROT + TrEMBL) data and
motif search against Pfam data in Janualy 2001. Annotations for FANTOM DB1.1
were updated based on these results. 

2.2. Association between RIKEN clones and MGI Makers
We have updated MGI maker association for 880 RIKEN clones based on 
Nomenclature report on the MGI FTP Server
(ftp://ftp.informatics.jax.org/pub/informatics/reports/archive/nomen/).

2.3. Annotation update based on latest annotation of MGI Maker related to RIKEN FANTOM clones. 
Riken-definitions and gene_symbols for 1089 RIKEN clones were changed based on 
Gene name and Symbols for MGI Makers respectively which were curated by MGI 
group's effort. 

3. Database access/Data Distribution

3.1. FANTOM annotation viewer
Each annotation results can be viewed through FANTOM viewer 
(http://fantom.gsc.riken.go.jp/viewer/). These results can be searched by ID or 
keyword(s) or Pfam Domain Name or TIGR Cellular role. 

3.2. FTP server
FANTOM data archive were available at FTP server (ftp://fantom.gsc.riken.go.jp/)

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Copyright Notice

The RIKEN makes no representation about the suitability or accuracy of FANTOM data 
or software for any purpose and makes no warranties. Either express or implied, 
including merchantability and fitness for a particular purpose or that the use of 
FANTOM data or software will not infringe any third party patents, copyrights, 
trademarks, or other rights. The software and data are provided "as is".

This software is provided for non-commercial purpose in the scientific community.
Any reproduction or use for commercial purpose is prohibited without permissions of
the Institute of Physical and Chemical Research (RIKEN) and NTT Software Corporation. 

For further information, please contact: fantom-help@gsc.riken.go.jp 

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Citation
To cite resources available from the FANTOM web site in your publications, use a
following format. 

The RIKEN Genome Explosion Research Group Phase II Team and the FANTOM Consortium
Functional annotation of a full-length mouse cDNA collection
Nature 409:685-690, 2001

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Acknowledgement
FANTOM DB 1.0 (released on February 8th) were prepared by
*The RIKEN Genome Explosion Research Group Phase II Team
*The FANTOM Consortium. 

FANTOM DB 1.1 (released on October 4th) has been prepared by
*FANTOM-help (mainly contributed by Masaaki Furuno, Takeya Kasukawa, Katsunaga Sakai, and Toshihisa Okido)
*the RIKEN Genome Explosion Research Group Phase II Team

We also thank MGI group whose collaboration is gratefully acknowledged.

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Contact address

FANTOM-help
Genome Exploration Research Group
Genomic Sciences Center
RIKEN (The Institute of Physical and Chemical Research) 
Yokohama Institute
1-7-22,Suehiro-cho, Tsurumi-ku
YOKOHAMA, 230-0045 
Japan
Phone: +81-45-503-9222
Fax: +81-45-503-9216
Email: fantom-help@gsc.riken.go.jp 
FANTOM DB web site:http://fantom.gsc.riken.go.jp/