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. |
| SPECIES | Species |
| 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 |
| ADMINISTRATION_ROUTE_TYPE | Administration route |
| ANIMAL_AGE(week) | Age of animal (weeks). Only rats at 6 weeks of age were used. |
| SACRIFICE_PERIOD | Sampling time or period. |
| DOSE | Dose |
| DOSE_UNIT | Unit of dose |
| DOSE_LEVEL | Dose level. The ascending order of the levels is Control, Low, Middle, High. |