Example Data Files
Example Input Data
Example data files allow testing and review of the application. The data format requirements for each microarray platform is shown following Table 1 below. To analyze example data:
- Download and save the example data file(s) you wish to test
- In the "Study Information" section, select any option for the data fields displayed or use default information displayed
- Select the microarray platform corresponding to the data file to be uploaded
- In the "File Upload" section, select "Test Chemical" as Test type
- Enter any information you wish in the required fields "Test chemical name," "Concentration," and "Graph label name," e.g. Chemical 1, 100 ppm, Chem-1 (data in required fields are used in output results)
- Select and upload the data file(s) requested for the microarray platform chosen and click [Submit] to begin data analysis
- If "Generic Array" is selected, the column number in which the transformed log(2) ratios are recorded must be specified in the "Log(2) ratio column" field
- Click [Submit] to begin data analysis
-
If "Batch Data" is selected as the Microarray platform:
- Only "Test chemical name" and the data file are required. When the batch data file has data for more than one chemical, the "Test chemical name" should represent the data set (e.g., Alkylators)
- Clicking [Submit] now displays a table showing the information, derived from the data file, to be used in the output results
- Review this information in the table for accuracy and completeness, then click [Start Process] to begin data analysis
Format Requirements
| Microarray Platform | Download Files | Format | Classification |
|---|---|---|---|
| Affymetrix Human Genome U133 Plus 2.0 Array |
Control (CEL) Treatment (CEL) |
.CEL | DDI |
| Agilent Whole Human Genome Microarray 8x60K Dye Swap |
Dye Swap Cy5 to Cy3 Dye Swap Cy3 to Cy5 |
.txt | NDDI |
| Agilent Whole Human Genome Microarray 8x60K Two-Color Treated Cy5 |
Treated (Cy5) to control (Cy3) |
.txt | NDDI |
| Agilent Whole Human Genome Microarray 8x60K Two-Color Treated Cy3 |
Treated (Cy3) to control (Cy5) |
.txt | NDDI |
| Agilent Whole Human Genome Microarray 8x60K One-Color |
Treatment Control |
.txt | DDI |
| Generic Array |
Generic |
.txt | NDDI |
| Batch data |
Batch Data (4 data points) Batch Large Dataset (100 data points) |
.xlsx | Varies |
Generic Data File Format Requirements
Data must be normalized log2 transformed data saved as a tab-delimited text file. Probe ids should be in column one followed by the data in subsequent columns which are labeled according to data type (e.g., treated, control, chemical) and/or concentration.
| Probe | NTHi.treated.LR-CC | NTHi.treated.WT | OVA.treated.LR-CC | OVA.treated.WT |
|---|---|---|---|---|
| Aaas | -0.262378693599992 | 0.146432693658835 | -0.157264050379592 | -0.0651864466863898 |
| Aacs | -1.53491245721088 | 1.10814149987023 | -1.2157214508298 | 0.418492940073264 |
| Aadac | -0.0586933881927107 | 0.1442209728927 | 0.0788273928233627 | -0.0923946951609533 |
| Aadacl1 | -0.733289451992194 | 0.62914735709511 | -0.632552945614945 | -0.492177435976563 |
| Aadat | -0.159316061603705 | 0.0613344138502185 | -0.115660975691996 | 0.0753399558126331 |
| Aak1 | 0.0904840090828394 | 0.0556915318859392 | 0.221756142818329 | 0.0216089565332158 |
| Zxda | 2.45091984025087 | 0.120654237438437 | 3.34296788358073 | 0.320819430417137 |
| Zyg11b | -0.0478395460279151 | 0.651829709531177 | 0.0557371282639751 | 0.0712314806347631 |
| Zyx | 0.374573669921801 | 0.407195369109495 | 0.205405113752109 | 0.163212746980367 |
| Zzz3 | 0.0391893916866923 | 0.259348251462574 | -0.17440149935954 | 0.0577744934435049 |
Batch Data Format Requirements
Input Data File in Excel format
Similar to the generic, text file format, the Excel file needs the probe ids listed in column one followed by normalized log2 data in the subsequent columns, which are labeled according to data listed using chemical name or ID-concentration and unit (e.g., BaP-10 ug/ml).
| Probe | EX-Chem1-9.5 nM | EX-Chem1-30 nM | EX-Chem1-94.8 nM | EX-Chem2-9.5 nM | EX-Chem2-30 nM | EX-Chem2-94.8 nM | EX-Chem3-9.5 nM | EX-Chem3-30 nM | EX-Chem3-94.8 nM |
|---|---|---|---|---|---|---|---|---|---|
| A2M | -1.119397338 | -1.36567208 | -1.450002669 | -1.163527699 | -1.305211255 | -1.562601604 | -1.203126958 | -1.111288448 | -1.189491073 |
| ABCC5 | -1.126163788 | -1.175751631 | -1.2698331 | 1.006176454 | 1.101222167 | 1.152238117 | 1.057812063 | 1.023433006 | 1.104773026 |
| ABCG1 | 1 | 1 | 1 | 1 | 1 | 1.026057165 | 1 | 1 | 1 |
| APOE | -1.106667803 | -1.307671349 | -1.373636233 | -1.188026211 | -1.200720197 | -1.414660195 | 1.042606272 | -1.036561385 | 1.151067328 |
| ARNT2 | -1.118083378 | 1.099213953 | -1.133342043 | -1.03810729 | -1.044925438 | 1.049506507 | 1.105432636 | -1.022310422 | -1.118966362 |
| ZMIZ1 | -1.268879928 | -1.241092901 | -1.499692447 | -1.199176856 | -1.500894137 | -1.642672006 | -1.440291783 | -1.205923917 | -1.220405943 |
| ZNF318 | -1.00387757 | -1.00387757 | -1.00387757 | 1.002776436 | 1 | 1 | 1 | 1.033193957 | 1 |
| ZNF395 | 1.21288641 | -1.126055377 | -1.045601658 | -1.207220231 | -1.19731271 | -1.303066861 | -1.34888955 | -1.242857687 | 1.021645331 |
| ZNF420 | 1.010179109 | -1.009634653 | 1.059748719 | 1 | 1.041823663 | 1 | 1 | 1 | 1.002621987 |
| ZWINT | -1.097205176 | 1.412417564 | 1.189985871 | -1.035835167 | -1.046903001 | 1.006323699 | -1.431207977 | -1.165370656 | -1.42143137 |
Results Table Download
The results table is downloaded as a tab-delimited text file. The results are displayed in nine columns: Class, DDI Probability, NDDI Probability, Test Type, Chemical Name, Concentration, Cell Line, Sample Time, Platform, Submitted File(s), and Submission ID.
| Class | DDI Probability | NDDI Probability | Test Type | Chemical Name | Concentration | Cell Line | Sample Time | Platform | Submitted File(s) | Submission ID |
|---|---|---|---|---|---|---|---|---|---|---|
| Non DNA Damage Inducing | 2.55E-12 | 1 | Test chemical | EX-Chem1_1 | 9.5 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_de08 |
| Non DNA Damage Inducing | 4.35E-36 | 1 | Test chemical | EX-Chem1_2 | 30 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_ogrq |
| Non DNA Damage Inducing | 1.30E-32 | 1 | Test chemical | EX-Chem1_3 | 94.8 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_8n5z |
| Non DNA Damage Inducing | 2.79E-57 | 1 | Test chemical | EX-Chem2_4 | 9.5 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_ktpf |
| Non DNA Damage Inducing | 4.10E-43 | 1 | Test chemical | EX-Chem2_5 | 30 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_ebos |
| Non DNA Damage Inducing | 1.87E-92 | 1 | Test chemical | EX-Chem2_6 | 94.8 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_55jq |
| Non DNA Damage Inducing | 3.35E-111 | 1 | Test chemical | EX-Chem3_7 | 9.5 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_2xsb |
| Non DNA Damage Inducing | 1.08E-101 | 1 | Test chemical | EX-Chem3_8 | 30 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_x518 |
| Non DNA Damage Inducing | 3.69E-101 | 1 | Test chemical | EX-Chem3_9 | 94.8 nM | TK6 | 4 hr | Generic Array | Batch_Lg_Dataset.xlsx | 20180115_7u9g |
NOTE: "Chemical Name" and "Concentration" are derived from the column headers of the data input file with an underscore and sequential number appended to each name.
- .CEL
- A binary data output from Affymetrix
- .txt
-
Tab-delimited files from Agilent output, or
User-generated normalized log(2) transformed data - .xlsx
- User-generated Excel files containing normalized log(2) transformed data
- DDI
- DNA Damage-Inducing
- NDDI
- Non DNA Damage-Inducing