6. Appendix 1

Descriptions of the fields in the TG-GATEs gene expression file

Information was obtained from: ftp://ftp.biosciencedbc.jp/archive/open-tggates/LATEST/README_e.html. Note that not all of the id types are relevant for the in vitro data which is made using human samples in our case.

CEL file attributes

Data name CEL file attributes
Description of data contents List of attribute information explain about each CEL file.
File open_tggates_cel_file_attribute.zip (199 KB)

Data items are the following:

Data item Description
BARCODE Bar-code assigned to each GeneChip in order to indentify. Bar-code matches CEL file name without extension.
ARR_DESIGN In the project, HG-U133_Plus_2 was used for human and Rat230_2 was used for rat.
EXP_ID ID assigned to each test which can be indentified by a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are assigned from #0040. IDs for in vitro tests are assigned from #5000.
GROUP_ID ID assigned to each group which can be identified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16)
INDIVIDUAL_ID ID assigned to each individual/sample within a group. IDs are in single digit.
ORGAN Organ evaluated in tests. Liver or Kidney.
MATERIAL_ID ID assigned to each tissue section which was used to acquire gene expression data. IDs are in a single letter.
COMPOUND_NAME Compound name
COMPOUND_ABBREVIATION Abbreviated compound name
COMPOUND_NO Number assigned to each compound. Numbers are not in serial order.
EXP_TEST_TYPE Type of test. In vivo test or in vitro test.
SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test.
SEX_TYPE Gender. Male or Female.
STRAIN_TYPE Rat strain used with in vivo tests
ANIMAL_AGE(week) Age of animal (weeks). Only rats at 6 weeks of age were used.
SACRIFICE_PERIOD Sampling time or period.
DOSE_UNIT Unit of dose
DOSE_LEVEL Dose level. The ascending order of the levels is Control, Low, Middle, High.