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 |