Identification of hub miRNA biomarkers for bladder cancer by weighted gene coexpression network analysis

Figures & data

Figure 1 Volcano plot of differentially expressed miRNAs.

Abbreviations: FC, fold change; FDR, false discovery rate.

Figure 2 Identification of key modules associated with the progression of BC.

Notes: (A) Results of a cluster analysis and five modules identified from DEM expression networks. (B) The blue module had the highest mean gene significance among these modules. (C) Relationship between gene significance and intramodular connectivity.
Abbreviations: BC, bladder cancer; DEMs, differentially expressed miRNAs.

Table 1 Top 25% of the 54 miRNAs showing the highest connectivity and MM values in the blue module

microRNA	Module	Connectivity	Module membership
hsa-miR-133a-1	Blue	14.52815127	0.942911887
hsa-miR-133a-2	Blue	14.13870062	0.931813002
hsa-miR-1–2	Blue	13.22743045	0.921363767
hsa-miR-1–1	Blue	13.2169924	0.920517623
hsa-miR-133b	Blue	12.77790952	0.914496915
hsa-miR-143	Blue	11.9099187	0.890564772
hsa-miR-195	Blue	11.52715541	0.868339224
hsa-miR-139	Blue	11.20058022	0.854359765
hsa-miR-6507	Blue	10.72163066	0.82522312
hsa-miR-145	Blue	10.39113951	0.801384187
hsa-miR-28	Blue	10.24439735	0.8227846
hsa-miR-3199–2	Blue	9.044028532	0.818183518
hsa-miR-548ba	Blue	8.813461621	0.812107848

Abbreviation: MM, module membership.

Figure 3 A network of hub miRNAs and their target genes.

Notes: The cumulative weighted context++ scores, which indicate how effectively a given miRNA may target mRNAs, are shown by the node color. The figure was generated using CytoScape.

Figure 4 Functional annotations of the target genes.

Notes: (A) The 27 enriched GO biologic process terms. (B) The 17 enriched KEGG pathways.
Abbreviations: GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 5 TAGLN2 is upregulated in human BC specimens.

Notes: (A, B) TAGLN2 expression in normal bladder tissue and BC specimens. (C) TAGLN2 expression in the TCGA BC RNAseq dataset (N=408). (D) Oncomine data showing TAGLN2 expression in normal (n=48) vs tumor (n=81) bladder specimens. (E) One-way ANOVA analysis showed that TAGLN2 expression levels were significantly associated with TNM stage in the TCGA BC RNAseq dataset.
Abbreviations: ANOVA, analysis of variance; BC, bladder cancer; N, normal; TCGA, The Cancer Genome Atlas; T, tumor.

Table 2 Overall survival of the hub miRNAs in the blue module

Hub miRNA	HR (95% CI)	P-value
hsa-miR-133a-1	1.372 (1.026–1.834)	0.0327
hsa-miR-133a-2	1.284 (0.961–1.716)	0.0921
hsa-miR-1–2	1.205 (0.902–1.610)	0.2069
hsa-miR-1–1	1.222 (0.9146–1.633)	0.1759
hsa-miR-133b	1.530 (1.145–2.045)	0.0498
hsa-miR-143	1.597 (1.195–2.134)	0.0018
hsa-miR-195	1.452 (1.086–1.940)	0.0127
hsa-miR-139	1.133 (0.848–1.514)	0.3977
hsa-miR-6507	1.585 (1.186–2.118)	0.0020
hsa-miR-145	1.705 (1.276–2.279)	0.0004
hsa-miR-28	0.823 (0.6159–1.100)	0.1878
hsa-miR-3199–2	1.107 (0.828–1.479)	0.5110
hsa-miR-548ba	1.408 (1.054–1.882)	0.0212

Note: Bold type indicates statistical significance.

Abbreviations: CI, confidence interval; HR, hazard ratio.