This directory contains the data used in the FANTOM4 collaborative research.


Directory structure
-------------------

* Meta-data : the detailed information about experimental protocol and flow.

* human     : data files for human cells

* mouse     : data files for mouse cells



File format
-----------

* Already defined format, such as GFF, SGR (affy IGB's format), BED, XLSX, etc.

* In most cases, we use text files formated (*.tbl.txt) as:

  - Tab-delimted text

  - Lines starting with '#' are used to describe comments in free format.

  - Lines starting with '##' are used to describe information in a defined way
    ('qualifier = value'). In particular, each column is described as:

      ##ColumnVariable[COLUMN_NAME] = [DESCRIPTION]

  - Column names are specified in the first line after '#' or '##' starting lines




Citation
---------

Please cite the following paper(s) when you use the data files here,
in addition to the relevant papers in http://fantom.gsc.riken.jp/4/publications/

* Kawaji H, Severin JM, Lizio M, Waterhouse AM, Katayama S, Irvine KM,
  Hume DA, Forrest ARR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO.,
  "The FANTOM Web Resource: from mammalian transcriptional landscape to its dynamic regulation",
  Genome Biology. 2009, 10:R40