Panel of seven long noncoding RNA as a candidate prognostic biomarker for ovarian cancer

Figures & data

Figure 1 Study workflow showing the order of lncRNA analyses applied to develop a risk score model and use of the model to predict prognostic information and validate the efficiency of the signature panel.

Abbreviations: GSEA, Gene Set Enrichment Analysis; lncRNA, long non-coding RNA.

Figure 2 Random survival forests variable hunting analysis.

Notes: (A) Error rate for the data as a function of trees; (B) out-of-bag importance values for predictors.

Table 1 Seven lncRNAs significantly associated with the overall survival in the training set (n=278)

Gene symbol	Parametric, P-value	Hazard ratio (95% CI)	Coefficient	Variable importance	Relative importance
BC037530	2.30e–05*	2.6345 (1.6824–4.1255)	0.3411	0.0142	1
AK021924	0.0004	1.6518 (1.2529–2.1776)	0.4767	0.0125	0.8803
BC007937	0.0006	0.0822 (0.0198–0.3418)	−1.9507	0.0111	0.7817
AK094536	0.0002	1.9171 (1.3573–2.7077)	0.1509	0.0089	0.6268
BC062365	0.0007	1.7997 (1.2812–2.5280)	0.2081	0.0076	0.5352
AK130460	0.0005	2.1251 (1.3862–3.2577)	0.5741	0.0063	0.4427
BC004123	0.0004	0.5137 (0.3558–0.7417)	−0.6688	0.0036	0.2535

Note:

* P-value formatting as per the following example: 2.30e–05 is 0.000023.

Abbreviations: CI, confidence interval; lncRNAs, long non-coding RNAs.

Figure 3 Kaplan–Meier was used to estimate the survival of high-risk vs low-risk ovarian cancer patients based on the seven-lncRNA signature.

Notes: (A) The OS for GSE9891; (B) the OS for GSE26193; (C) the OS for GSE63885; (D) the PFS for GSE9891; (E) the PFS for GSE26193; (F) the disease-free survival for GSE63885.
Abbreviations: OS, overall survival; PFS, progression-free survival; lncRNA, long noncoding RNA.

Figure 4 lncRNA risk score analysis of the GSE9891 patients.

Notes: (A) lncRNA risk score distribution; (B) the distribution of patients overall survival status and time; (C) heatmap of the seven-lncRNA expression profiles. Rows represent lncRNAs and columns represent patients. The black dotted line represents the median lncRNA risk score which was used as cutoff to divide patients into high-risk and low-risk groups.
Abbreviation: lncRNA, long noncoding RNA.

Table 2 Univariate and multivariate Cox regression analyses of OS in each data set

Variables	Univariate model			Multivariate model
	HR	95% CI of HR	P-value	HR	95% CI of HR	P-value
Training set (GSE9891, N=278)
lncRNA risk score (high risk vs low risk)	2.80	1.88–4.17	4.68e–07*	2.35	1.55–3.55	4.99e–05*
Age	1.03	1.01–1.05	0.0134	1.02	1.00–1.04	0.0435
Tumor grade	1.32	0.96–1.81	0.0852	1.20	0.86–1.68	0.2814
FIGO stages (I/II/III/IV)	2.17	1.50–3.15	4.49e–05*	1.77	1.20–2.60	0.0039
Testing set (GSE26193, N=107)
lncRNA risk score (high risk vs low risk)	2.16	1.36–3.43	0.0011	1.48	0.91–2.40	0.114
Tumor grade	1.21	0.83–1.76	0.326	0.72	0.48–1.08	0.109
FIGO stages (I/II/III/IV)	2.06	1.54–2.74	1.03e–06*	2.09	1.52–2.88	5.68e–06*
Testing set (GSE63885, N=75)
lncRNA risk score (high risk vs low risk)	1.59	0.98–2.59	0.0623	1.56	0.94–2.59	0.0886
Tumor grade	1.71	1.13–2.58	0.0113	1.75	1.14–2.69	0.0111
FIGO stages (I/II/III/IV)	2.32	1.24–4.32	0.0085	1.90	0.99–3.67	0.0547

Notes: The age information was only available in the GSE9891 set.

* P-value formatting as per the following example: 4.68e-07 is 0.000000468. P-values <0.05 are significant.

Abbreviations: OS, overall survival; HR, hazard ratio; CI, confidence interval; lncRNA, long non-coding RNA; FIGO, Federation of Gynecology and Obstetrics.

Table 3 Univariate and multivariate Cox regression analyses of PFS/DFSin each data set

Variables	Univariate model			Multivariate model
	HR	95% CI of HR	P-value	HR	95% CI of HR	P-value
Training set (GSE9891, N=275)
lncRNA risk score (high risk vs low risk)	2.10	1.57–2.83	7.22e–07*	1.75	1.29–2.38	0.0003
Age	1.01	1.00–1.03	0.13	1.01	1.00–1.03	0.1891
Tumor grade	1.27	1.00–1.62	0.0466	1.22	0.94–1.57	0.1342
FIGO stages (I/II/III/IV)	2.34	1.78–3.07	9.26e–10	2.09	1.58–2.76	2.01e–07*
Testing set (GSE26193, N=107)
lncRNA risk score (high risk vs low risk)	1.78	1.14–2.78	0.012	1.21	0.76–1.92	0.433
Tumor grade	1.41	0.96–2.06	0.0775	0.84	0.55–1.28	0.407
FIGO stages (I/II/III/IV)	1.96	1.51–2.54	4.46e–07*	2.00	1.48–2.69	4.89e–06*
Testing set (GSE63885, N=75)
lncRNA risk score (high risk vs low risk)	2.30	1.39–3.79	0.0011	2.10	1.27–3.48	0.0041
Tumor grade	1.59	1.05–2.41	0.0279	1.65	1.08–2.51	0.0205
FIGO stages (I/II/III/IV)	2.71	1.44–5.11	0.0020	2.40	1.24–4.64	0.0092

Notes: The age information only existed in GSE9891 set.

* P-value formatting as per the following example: 7.22e-07 is 0.000000722. P-values <0.05 are significant.

Abbreviations: PFS, progression-free survival; DFS, disease-free survival; HR, hazard ratio; CI, confidence interval; lncRNA, long non-coding RNA; FIGO, Federation of Gynecology and Obstetrics.

Figure 5 ROC analysis of sensitivity and specificity for seven-lncRNA risk score, FIGO stage and patient age in training set.

Note: The AUROCs of seven-lncRNA risk score vs FIGO stage and patient age were 0.742, 0.626 and 0.534, respectively.
Abbreviations: ROC, receiver operating characteristic; lncRNA, long noncoding RNA; AUROC, area under ROC; FIGO, Federation of Gynecology and Obstetrics.

Figure 6 GSEA analysis of high-risk group.

Notes: (A) The barplot of the signaling pathways significant enriched in the high-risk group; (B) enrichment plot of ECM–receptor interaction; (C) enrichment plot of focal adhesion; (D) enrichment plot of TGF-beta signaling pathway.
Abbreviations: ECM, extracellular matrix; FWER, family-wise error rate; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; TGF, transforming growth factor.