TABLE 4.
Summary of candidate genes identified by the various methods used
| Method | Significance level | Condition | No. of genes/ proteins | Total no. of genes/ proteinsa |
|---|---|---|---|---|
| Microarray | FDR = 0.05 | Over all chromosomes | 11,223 | 24,530b |
| Microarray | FDR = 0.0001 | Over all chromosomes | 831 | 24,530b |
| Microarray | FDR = 0.0001 | In QTL | 87 | 3,763c |
| Proteomics | P < 0.1 | Over all chromosomes | 45 | 943 |
| Proteomics | P < 0.1 | In QTL region | 5 | Unknownd |
| SNP analysis | NA | In QTL and non-IBD region | 336 | 2,752 |
a
Gene here also refers to an Affymetrix probe for the microarrays and a peptide linked to a protein entry in the Swiss-Prot or TrEMBL databases for the proteomics.
b
There are 45,037 noncontrol probe sets on the arrays; however, 20,507 are not expressed in any of the six samples, indicating that genes for those probes are not expressed in adult female mouse liver.
c
The total number of probes within the total space of the nine QTL including IBD regions between SM and NZB.
d
Many protein hits could not be mapped to genomic locations so the genes located only in QTL regions cannot be determined.