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Table 1 Output from BMDExpress Characterizing the Dose-dependent Behavior of Each GO Category

From: BMDExpress: a software tool for the benchmark dose analyses of genomic data

Output from GO Analysis Description of Output
GO Level Level in the hierarchy of the GO category
GO Term Name Official name of the GO category
All Genes Total number of genes on the array assigned to the GO category
Genes from BMD Analysis Number of genes from BMD analyses in the GO category
Percentage Percentage of the total number of genes in GO category used in BMD analysis
Gene IDs Entrez Gene identifiers in GO category based on Affymetrix probe set identifiers from BMD analysis
Probe IDs Affymetrix probe set identifiers from BMD analysis
BMD Mean Mean BMD for the genes in GO category
BMD Median Median BMD for the genes in GO category
BMD Minimum Minimum BMD for the genes in GO category
BMD SD Standard deviation of BMD for the genes in GO category
BMD wMean Weighted mean BMD for the genes in GO category (weighted by fit p-value)
BMD wSD Standard deviation of the weighted mean BMD for the genes in GO category (weighted by fit p-value)
BMDL Mean Mean BMDL for the genes in GO category
BMDL Median Median BMDL for the genes in GO category
BMDL Minimum Minimum BMDL for the genes in GO category
BMDL SD Standard deviation of the BMDL for the genes in GO category
BMDL wMean Weighted mean BMDL for the genes in GO category (weighted by fit p-value)
BMDL wSD Standard deviation of the weighted mean BMDL for the genes in GO category (weighted by fit p-value)
5th Percentile Index Nth gene number representing the 5th percentile for all the genes in the category. The value is zero-based and a 0.5 value means that it falls between two values
BMD at 5th Percentile BMD at the 5th percentile for all genes in the GO category (including genes with no significant dose response)
10th Percentile Index Nth gene number representing the 10th percentile for all the genes in the category. The value is zero-based and a 0.5 value means that it falls between two values
BMD at 10th Percentile BMD at the 10th percentile for all genes in the GO category (including genes with no significant dose response)
Probes with Adverse Direction Up Number of probe sets in the GO category for which the final change in expression was in the up (i.e., increased) direction
Probes with Adverse Direction Down Number of probe sets in the GO category for which the final change in expression was in the down (i.e., decreased) direction