Open TG-GATEs
2012/07/04
HTTPS Site:
https://dbarchive.biosciencedbc.jp/data/open-tggates/
The database of gene expression and toxicity when exposing rats and rat and human liver cells to 170 compounds.
README Content
- Database Component
- Data Description
- License
- Update History
- Literature
- Contact address
1. Database Component
- README
- Compound list
- Gene expression data (CEL files)
- CEL file attributes
- Cell sample
- Cell viability
- Individual list
- Organ weight
- Hematology
- Biochemistry
- Body weight
- Food consumption
- Pathology items
2. Data Description
2.1 README
| Data name |
README |
| Description of data contents |
HTML file to describe "Open TG-GATEs" data. |
| File |
README_e.html(English) |
2.2 Compound list
| Data name |
Compound list |
| Description of data contents |
Compiled list of compounds and links to gene expression data and its attribute information of each compound in Open TG-GATEs. |
| File |
open_tggates_main.zip (6.4 KB) |
Data items are the following:
| Data item |
Description |
| COMPOUND_NAME |
Compound name |
| COMPOUND_ABBREVIATION |
Abbreviated compound name |
| COMPOUND_NO |
Number assigned to each compound. Numbers are not in serial order. |
| Human - in vitro |
Gene expression data of in vitro tests with human liver cells (Link to a zip file which contains multiple CEL files) |
| Rat - in vitro |
Gene expression data of in vitro tests with rat liver cells (Link to a zip file which contains multiple CEL files) |
| Rat - in vivo - Liver - Single |
Gene expression data of single-dose in vivo tests with rat liver (Link to a zip file which contains multiple CEL files) |
| Rat - in vivo - Liver - Repeat |
Gene expression data of repeat-dose in vivo tests with rat liver (Link to a zip file which contains multiple CEL files) |
| Rat - in vivo - Kidney - Single |
Gene expression data of single-dose in vivo tests with rat kidney (Link to a zip file which contains multiple CEL files) |
| Rat - in vivo - Kidney - Repeat |
Gene expression data of repeat-dose in vivo tests with rat kidney (Link to a zip file which contains multiple CEL files) |
| Pathological items (Liver) |
Pathological findings and slide images of in vivo tests with rat liver (Link to "Pathological items", "Pathological images" and "CEL file attributes") |
| Pathological items (Kidney) |
Pathological findings and slide images of in vivo tests with rat kidney (Link to "Pathological items", "Pathological images" and "CEL file attributes") |
2.3 Gene expression data (CEL files)
| Data name |
Gene expression data (CEL files) |
| Description of data contents |
CEL files available in Open TG-GATEs are grouped by the test, and then they are compressed separately into a zip file. In each zip file, a CEL file attribute file in Tab Separated Value (TSV) format is included.
CEL is one of the file formats that expresses gene expression data (raw data) generated from Affymetrix GeneChip®. |
| File |
File name: Gene expression data from rat samples
File URL: https://dbarchive.biosciencedbc.jp/data/open-tggates/LATEST/Rat/
File size: 12.0GB total
File name: Gene expression data from human samples
File URL: https://dbarchive.biosciencedbc.jp/data/open-tggates/LATEST/Human/
File size: 53.6GB total |
2.4 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 indentified 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. |
2.5 Cell sample
| Data name |
Cell sample |
| Description of data contents |
The list of liver cell samples from which gene expression and toxicity (cell viability) data were acquired. |
| File |
open_tggates_cell.zip (54 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) |
| INDIVIDUAL_ID |
ID assigned to each sample within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| SPECIES |
Species |
| SEX_TYPE |
Gender. Male or Female. |
| SACRIFICE_PERIOD |
Duration of exposure on in vitro test. |
| DOSE |
Concentration |
| DOSE_UNIT |
Unit of concentration |
| DOSE_LEVEL |
Exposure level. The ascending order of the levels is Control, Low, Middle, High. |
| BARCODE |
Link to "CEL file attributes" |
| CELL_VIABILITY |
Link to "Cell viability" |
2.6 Cell viability
| Data name |
Cell viability |
| Description of data contents |
The list of liver cell viability data obtained from in vitro tests. |
| File |
open_tggates_cell_viablity.zip (51 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified by a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16) |
| INDIVIDUAL_ID |
ID assigned to each sample within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| SPECIES |
Species |
| SEX_TYPE |
Gender. Male or Female. |
| SACRIFICE_PERIOD |
Duration of exposure on in vitro test. |
| DOSE |
Concentration |
| DOSE_UNIT |
Unit of concentration |
| DOSE_LEVEL |
Exposure level. The ascending order of the levels is Control, Low, Middle, High. |
| DNA(%) |
Relative survival rate calculated from DNA content. |
| LDH(%) |
Relative survival rate calculated from the activity value of lactate dehydrogenase which is leaked in the culture supernatant. |
2.7 Individual list
| Data name |
Individual list |
| Description of data contents |
The list of rats from which gene expression and toxicity data were acquired. |
| File |
open_tggates_individual.zip (97 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| 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 on in vivo test. |
| DOSE |
Dose |
| DOSE_UNIT |
Unit of dose |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| BARCODE (Liver) |
Link to "CEL file attributes (Liver)" |
| BARCODE (Kidney) |
Link to "CEL file attributes (Kidney)" |
| HEMATOLOGY |
Link to "Hematology" |
| BIOCHEMISTRY |
Link to "Biochemistry" |
| ORGAN_WEIGHT |
Link to "Organ weight" |
| BODY_WEIGHT |
Link to "Body weight" |
| FOOD_CONSUMPTION |
Link to "Food consumption" |
| PATHOLOGY (Liver) |
Link to "Pathological items (Liver)" |
| PATHOLOGY (Kidney) |
Link to "Pathological items (Kidney)" |
| PATHOLOGICAL_IMAGE (Liver) |
Link to "Pathological images (Liver)" |
| PATHOLOGICAL_IMAGE (Kidney) |
Link to "Pathological images (Kidney)" |
2.8 Organ weight
| Data name |
Organ weight |
| Description of data contents |
The list of organ weights acquired from in vivo tests. Information of terminal body weights is also included. |
| File |
open_tggates_organ_weight.zip (379 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| 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 on in vivo test. |
| DOSE |
Dose |
| DOSE_UNIT |
Unit of dose |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| TERMINAL_BW(g) |
Terminal body weight |
| LIVER(g) |
The weight of the liver |
| KIDNEY_TOTAL(g) |
The total weight of the kidneys |
| KIDNEY_R(g) |
The weight of the right kidney |
| KIDNEY_L(g) |
The weight of the left kidney |
2.9 Hematology
| Data name |
Hematology |
| Description of data contents |
The list of hematological assessment data acquired from rats used in the in vivo tests. |
| File |
open_tggates_hematology.zip (636 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| SINGLE_REPEAT_TYPE |
Type of in vivo test. Single-dose test or 28-day repeat-dose test. |
| SACRIFICE_PERIOD |
Sampling time or period on in vivo test. |
| DOSE |
Dose |
| DOSE_UNIT |
Unit of dose |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| RBC(x10_4/ul) |
red blood cell count |
| Hb(g/dL) |
hemoglobin |
| Ht(%) |
hematocrit value |
| MCV(fL) |
mean corpuscular volume |
| MCH(pg) |
mean corpuscular hemoglobin |
| MCHC(%) |
mean corpuscular hemoglobin concentration |
| Ret(%) |
reticulocyte |
| Plat(x10_4/uL) |
platelet count |
| WBC(x10_2/uL) |
white blood cell count |
| Neu(%) |
neutrophil |
| Eos(%) |
eosinophil |
| Bas(%) |
basophil |
| Mono(%) |
monocyte |
| Lym(%) |
lymphocyte |
| PT(s) |
prothrombin time |
| APTT(s) |
activated partial thromboplastin time |
| Fbg(mg/dL) |
fibrinogen |
2.10 Biochemistry
| Data name |
Biochemistry |
| Description of data contents |
The list of biochemical test data acquired from rats used in the in vivo tests. |
| File |
open_tggates_biochemistry.zip (666 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| SINGLE_REPEAT_TYPE |
Type of in vivo test. Single-dose test or 28-day repeat-dose test. |
| SACRIFICE_PERIOD |
Sampling time or period on in vivo test. |
| DOSE |
Dose |
| DOSE_UNIT |
Unit of dose |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| ALP(IU/L) |
alkaline phosphatase |
| TC(mg/dL) |
total cholesterol |
| TG(mg/dL) |
triglyceride |
| PL(mg/dL) |
phospholipid |
| TBIL(mg/dL) |
total bilirubin |
| DBIL(mg/dL) |
direct bilirubin |
| GLC(mg/dL) |
glucose |
| BUN(mg/dL) |
blood urea nitrogen |
| CRE(mg/dL) |
creatinine |
| Na(meq/L) |
sodium |
| K(meq/L) |
potassium |
| Cl(meq/L) |
chlorine |
| Ca(mg/dL) |
calcium |
| IP(mg/dL) |
inorganic phosphorus |
| TP(g/dL) |
total protein |
| RALB(g/dL) |
albumin |
| A/G |
albumin globulin ratio |
| AST(IU/L) |
aspartate aminotransferase |
| ALT(IU/L) |
alanine aminotransferase |
| LDH(IU/L) |
lactate dehydrogenase |
| GTP(IU/L) |
γ-glutamyltranspeptidase |
2.11 Body weight
| Data name |
Body weight |
| Description of data contents |
Serial measurement of body weights of rats used in the in vivo tests. Information of slaughter weight is included in "Organ Weight". |
| File |
open_tggates_body_weight.zip (339 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| SACRIFICE_PERIOD |
Sampling time or period on in vivo test. |
| PROGRESS_TIME |
Measurement date of body weight. The unit is day. The day when the administration was started is counted as day 1. |
| BODY_WEIGHT |
Body weight of the rat on the day of PROGRESS_TIME. The unit is gram. |
2.12 Food consumption
| Data name |
Food consumption |
| Description of data contents |
The list regarding results of food consumption measurement acquired from rats used in the in vivo tests. |
| File |
open_tggates_food_consumption.zip (108 KB) |
Data items are the following:
| Data item |
Description |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| SACRIFICE_PERIOD |
Sampling time or period on in vivo test. |
| PROGRESS_TIME |
Measurement date of food consumption. The unit is day. The day when the administration was started is counted as day 1. |
| FC_AMOUNT |
The amount of daily food intake. The unit is gram per day (g/day). |
2.13 Pathological items
| Data name |
Pathological items |
| Description of data contents |
The list of pathological findings obtained from in vivo tests. |
| File |
open_tggates_pathology.zip (89 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. Data with the value "No ChipData" don't have a corresponding CEL file since the microarray gene expression analysis wasn't performed. |
| 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 indentified 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 within a group. IDs are in single digit. |
| COMPOUND_NAME |
Compound name |
| DOSE_LEVEL |
Dose level. The ascending order of the levels is Control, Low, Middle, High. |
| SACRIFICE_PERIOD |
Sampling time or period on in vivo test. |
| ORGAN |
Organ evaluated in tests. Liver or Kidney. |
| FINDING_TYPE |
Pathological findings. |
| TOPOGRAPHY_TYPE |
Region of the organ where the pathological changes were found. |
| GRADE_TYPE |
Magnitude of pathological changes. The ascending order of the magnitude is P(present), minimal, slight, moderate, severe. |
| SP_FLG |
The flag shows whether the lesion occurred spontaneously. The flag value is "1" if the lesion occurred spontaneously. |
| PATHOLOGICAL_IMAGE |
Link to "Pathological images" |
3. License
Last updated : 2012/05/24
You may use this database in compliance with the terms and conditions of the Standard License and the Additional License described below. The Standard License specifies the license terms regarding the use of this database and the requirements you must follow in using this database. The Additional License specifies those items that are exceptionally permitted even though they are generally prohibited in the Standard License.
Standard License
The Standard License for this database is the license specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "Toxicogenomics Project and Toxicogenomics Informatics Project under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other derivative works based on part or whole of the data from this database,
under the Standard License, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under this License.
Additional License
- You must display this Additional License along with the Standard License when distributing any derivative work based on part of whole of the data from this database.
- When you conduct research by using this database, and describe the research results in an article or paper, you always need to cite this database, and specify the name and URL of this database in the article or paper.
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the Standard License and the above Additional License.
National Institute of Biomedical Innovation
7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
Tel: +81-72-641-9826
E-mail: opentggates[at]nibio[dot]go[dot]jp
About Providing Links to This Database
You can freely provide links to all contents in this database. But, contents might be changed without notice.
4. Update History
| Date |
Update contents |
| 2012/07/04 |
A part of the hematology and biochemistry data obtained from the in vivo tests with rats is corrected.
For details, please refer to the following link.
Data correction |
| 2012/05/24 |
Open TG-GATEs English archive site is opened. |
| 2012/02/25 |
Open TG-GATEs(http://toxico.nibio.go.jp/) is released. |
5. Literature
-
6. Contact address
When you have any question about "Open TG-GATEs", contact the following:
Toxicogenomics Informatics Project, National Institute of Biomedical Innovation
7-6-8, Saito-asagi, Ibaraki-city, Osaka 567-0085, Japan
Tel: +81-72-641-9826
E-mail: opentggates[at]nibio[dot]go[dot]jp