Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD)
Fig 2
Filtering gene expression data significantly changes mean values for gene and pathway BMD(L)s.
The distributions of the BMD (left) and BMDL (right) values for genes (top), pathway means (center), and pathway medians (bottom), from the RNA-seq (yellow), microarray (aqua), and qPCR (pink) experiments, were compared. Upper and lower quartiles are indicated by box, the median is indicated by the line within the box and points represent outlier BMD(L) values (upper quartile + 1.5 x the inter quartile range (IQR) or the lower quartile—1.5 x IQR). Within each genomics platform, filtering significantly changed sample means (t-test p < 0.0001; S5 Table).