Table 3.
The DEx transcripts identified at the whole gene level and supported by the PBMs microarray dataset
| Discovery dataset (the RNA-seq dataset) | Supportive dataset (the microarray dataset) | |||||
|---|---|---|---|---|---|---|
|
| ||||||
| Transcript name | PPEE | PPDE | Direction of regulation1 | Probe set | P value | Direction of regulation2 |
| FCAR | 1.78E-15 | 1 | Up-regulation | 207674_at | 7.78E-04 | Up-regulation |
| 211307_s_at | 3.60E-02 | Up-regulation | ||||
| 211816_x_at | 4.88E-02 | Up-regulation | ||||
|
| ||||||
| CLCN5 | 0 | 1 | Up-regulation | 232127_at | 9.82E-03 | Up-regulation |
|
| ||||||
| CUX1 | 0 | 1 | Up-regulation | 202367_at | 2.14E-02 | Up-regulation |
| 227069_at | 2.19E-02 | Up-regulation | ||||
| 214743_at | 2.98E-02 | Up-regulation | ||||
| 225935_at | 4.12E-02 | Up-regulation | ||||
|
| ||||||
| RNASE3 | 0 | 1 | Up-regulation | 206851_at | 1.29E-02 | Up-regulation |
| REL | 7.77E-16 | 1 | Up-regulation | 206036_s_at | 1.75E-02 | Up-regulation |
| PXN-AS1 | 0 | 1 | Down-regulation | 227332_at | 1.95E-02 | Down-regulation |
| SGMS2 | 0 | 1 | Up-regulation | 242963_at | 2.02E-02 | Up-regulation |
| GGT1 | 0 | 1 | Up-regulation | 215603_x_at | 2.20E-02 | Up-regulation |
| HLA-DOA | 0 | 1 | Up-regulation | 217001_x_at | 2.94E-02 | Up-regulation |
| VNN2 | 0 | 1 | Up-regulation | 205922_at | 3.01E-02 | Up-regulation |
| ME1 | 0 | 1 | Up-regulation | 204059_s_at | 3.06E-02 | Up-regulation |
Note:
1
Direction of regulation in the RNA-seq dataset is defined based on the ratio of posterior mean expression in CP patients over controls, with a ratio of >1 as up-regulation and a ratio of <1 as down-regulation.
2
Direction of regulation in the microarray dataset is defined based on the ratio of mean expression 1 week before over 10 weeks after periodontal treatment (i.e., periodontally unhealthy over periodontally healthy statuses), with a ratio of >1 as up-regulation and a ratio of <1 as down-regulation.