Table 4. Most significant individual gene interaction networks ranked by permutation testing.
| Gene Family Member |
Enriched Genes
|
Cases
|
Controls
|
Gene Network Association
|
|||||
|---|---|---|---|---|---|---|---|---|---|
| No. | Frequency | No. | Frequency | # | Frequency | P fisher | Enrichment | P perm | |
| AKAP13 | 7/7 | 1.00 | 16 | 0.0035 | 1 | 0.0002 | 1.14E−04 | 16.43 | 0.012 |
| BAG1 | 7/7 | 1.00 | 15 | 0.0032 | 1 | 0.0002 | 2.18E−04 | 15.40 | 0.014 |
| CALM1 | 9/10 | 0.90 | 14 | 0.0030 | 1 | 0.0002 | 4.16E−04 | 14.37 | 0.002 |
| CASP6 | 16/17 | 0.94 | 46 | 0.0100 | 6 | 0.0013 | 2.96E−09 | 7.91 | 0.012 |
| GTF2H3 | 23/26 | 0.88 | 42 | 0.0091 | 8 | 0.0017 | 3.66E−07 | 5.41 | 0.009 |
| MAP3K5 | 11/12 | 0.92 | 34 | 0.0074 | 4 | 0.0008 | 2.02E−07 | 8.76 | 0.012 |
| NCOR1 | 9/10 | 0.90 | 26 | 0.0056 | 2 | 0.0004 | 1.11E−06 | 13.37 | 0.004 |
| PARP1 | 5/5 | 1.00 | 5 | 0.0011 | 0 | 0.0000 | 2.95E−02 | inf | 0.012 |
| PTPN13 | 6/6 | 1.00 | 9 | 0.0019 | 0 | 0.0000 | 1.75E−03 | inf | 0.007 |
| TCEA1 | 22/26 | 0.85 | 39 | 0.0084 | 7 | 0.0015 | 5.94E−07 | 5.74 | 0.009 |
The table lists the name and gene family member tested, the number and frequency of network genes enriched, the number and frequency of cases harbouring defects, the number and frequency of controls harbouring defects, and the significance of association by Fisher’s exact test, the odds ratio of the effect size, and the significance of association by random permutation of network while controlling for number of genes tested.