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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

Table 1. Example microarray platform file names, formats, and classifications
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.

Sample Generic data file format
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).

Sample Batch data file format
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.

Sample Result Table file format
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