Table 3.
Associations between parity in PVLSI and PBCS data sets and gene expression enrichment a
| PVLSI signature | SHL signature | UICH signature | ||||
|---|---|---|---|---|---|---|
| PVLSI normal tissues |
|
|
|
|||
| GSEA ESb |
0.98 |
-0.52 |
0.71 |
|||
| GSEA FWERb |
0% (sig) |
N/A |
3% (sig) |
|||
| Creighton analysisc |
Negative |
Positive |
Negative |
Positive |
Negative |
Positive |
| Nulliparous |
37 (69%) |
17 (31%) |
22 (41%) |
32 (59%) |
33 (61%) |
21 (39%) |
| Parous |
27 (36%) |
49 (64%) |
45 (59%) |
31 (41%) |
30 (39%) |
46 (61%) |
| OR (95% CI)d |
3.95 (1.88 to 8.29) |
0.47 (0.23 to 0.96) |
2.4 (1.18 to 4.92) |
|||
| P-valuee |
0.0002 (sig) |
N/A |
0.015 (sig) |
|||
| PBCS cancer-adjacent normal tissues |
|
|
|
|||
| GSEA ESb |
0.52 |
0.24 |
0.60 |
|||
| GSEA FWERb |
5% (sig) |
37% |
14% (sig) |
|||
| Creighton analysisc |
Negative |
Positive |
Negative |
Positive |
Negative |
Positive |
| Nulliparous |
17 (57%) |
13 (43%) |
16 (53%) |
14 (47%) |
15 (50%) |
15 (50%) |
| Parous |
58 (49%) |
61 (51%) |
62 (52%) |
57 (48%) |
62 (52%) |
57 (48%) |
| OR (95% CI)d |
1.38 (0.61 to 3.08) |
1.05 (0.47 to 2.34) |
0.92 (0.41 to 2.05) |
|||
| P-valuee |
0.44 |
0.90 |
0.84 |
|||
| PBCS tumor tissues |
|
|
|
|||
| GSEA ESb |
0.47 |
0.40 |
0.58 |
|||
| GSEA FWERb |
18% |
24% |
21% |
|||
| Creighton analysisc |
Negative |
Positive |
Negative |
Positive |
Negative |
Positive |
| Nulliparous |
16 (53%) |
14 (47%) |
14 (47%) |
16 (53%) |
21 (70%) |
9 (30%) |
| Parous |
58 (49%) |
61 (51%) |
55 (46%) |
64 (54%) |
65 (55%) |
54 (45%) |
| OR (95% CI)d |
1.20 (0.54 to 2.68) |
1.02 (0.56 to 2.27) |
1.94 (0.82 to 4.58) |
|||
| P-valuee | 0.65 | 0.96 | 0.13 | |||
aCI, Confidence interval; ES, Enrichment score; FDR, False discovery rate; FWER, Family-wise error rate; GSEA, Gene set enrichment analysis; OR, Odds ratio; N/A, Not applicable; PVLSI, Samples obtained from normal breast tissue of 130 women who underwent reduction mammoplasty surgery at Baystate Medical Center in Springfield, MA, USA, and banked at the Pioneer Valley Life Sciences Institute; SHL, Normal breast samples from 107 postmenopausal healthy volunteers recruited at the Sunderby Hospital in Luleå, Sweden; UICH, Mammoplasty benign biopsy specimens from 24 premenopausal women from the University of Illinois at Chicago Hospital. bIn GSEA analysis, ES indicates the GSEA enrichment score and FWER is the corresponding family-wise error rate and considered significant (sig) if ≤ 15%. cIn Creighton analysis, “Positive” and “Negative” indicate enriched and not enriched expression of parity signature, respectively. dIn Creighton analysis, odds ratios (ORs) and 95% confidence intervals (CIs) were obtained by unconditional logistic regression analysis with observed parity as the outcome variable and nulliparity as the reference. eIn Creighton analysis, P-values were obtained by χ2 test or Fisher’s exact test if the expected cell count was less than five, and considered significant (sig) if ≤ 0.05.