FAQ

1. Where can I get a list of non-coding cDNAs?
   
   - Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/noncoding/
2. Where can I get the transcribed genome regions defined by 5' and 3' ends?
   
   - Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/boundary_set/
3. Where can I get the GIS and GSC sequences?
   
   - Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/GIS/ and/or https://fantom.gsc.riken.jp/3/download/FANTOM3/GSC/
4. Where can I get the 5,154 new protein sequences?
   
   - Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/coding/
5. Different rearray IDs are derived for the same cDNA clone from ftp site (https://fantom.gsc.riken.jp/3/download/fantomdb/3.0/) and RIKEN cDNA annotation viewer https://fantom.gsc.riken.jp/3/db/. Why?
   
   - We have two types of rearray IDs for cDNA clones: for our sequencing, and for distribution of our cDNA clones on your request ( https://www.dnaform.jp/en/products/clone/fantom/ ). Rearray IDs in the clone distribution are accessible from the cDNA annotation viewer, while fantomdb 3.0 at the ftp site provides rearray IDs used in our cDNA sequencing. If you are interested in only cDNA clone sequences and/or functions, please use clone IDs, not rearray IDs.  For the purpose of bulk downloading the 'clone distribution' rearray IDs, https://fantom.gsc.riken.jp/3/ofc/Archive/FANTOM3setInfo.txt is also available.
6. How many bps would be transcribed when we approved aggressive strategy?
   
   - Please find here. https://fantom.gsc.riken.jp/3/download/FANTOM3/opt/forrest_aggressive/
7. Where can I find promoters determined by CAGE?
   
   - We classified CAGE tags and other 5'-end sequences into tag clusters (TC) to define promoters. You can look up tag cluster (TC) by CAGE analysis database (mouse and human)
8. Where can I download tag clusters (TCs) and their attributes?
   
   - All data in the CAGE basic and analysis databases are avaliable.  Tag clusters and their attributes are written in these files, tss_*.sql and tss_*.bz2, at the download directories of the CAGE Analysis database (mouse and human). Additional data used in our paper in Nature Genetics is available here, which contains classifications of tag clusters (TCs) based on the CAGE tag distirbution, and associations of tag clusters (TCs) with some promoter attributes.
9. Where can I download genomic coordinates used in FANTOM3?
   
   - Please take a look at here, before e-mailing to us. Esepcially, genomic coordinates of transcripts are included in 'alltrans.gff.bz2' or 'alltrans_symbolSynonym.gff.bz2' of the Genomic Elements Databases.