[Advanced] Analyzing in vitro toxicity and expression data (OK)


ToxCast is a project by the United States Environmental Protection Agency (EPA) aiming to “predict potential toxicity of chemicals and to develop a cost-effective approach for prioritizing the thousands of chemicals that need toxicity testing.” The project has made available a resource with different High Throughput Screening (HTS) data sets testing the toxicity of some 300 different chemicals.

One of the assays is the CellzDirect assay which tests for changes in transcription of 16 different genes. The assay contains 13440 datapoints and tests the effect of the different compound at five different concentrations (0.004-40 uM) at three different timepoints (6, 24, 48 hrs). The measurements are presented as fold change of the transcription levels and each measurement is done in four replicates.


  1. Your task is to compile a table with which chemical compound and at what concentration causes the highest fold change of transcription in each gene at each timepoint.The raw data can be downloaded from here.

The table should look similar to that below

Gene 6 hrs 24 hrs 48 hrs
ABCB1 Compound A, Conc Compound B, Conc Compound C, Conc