Exploration of the molecular mechanism of prostate cancer based on mRNA and miRNA expression profiles

Figures & data

Figure 1 Boxplots for gene expression of each sample in GSE46602 (A) and GSE55945 (B).

Figure 2 Venn diagram of the DEGs in GSE46602 and GSE55945 (A) and fold change correlation between the two datasets (B).

Abbreviation: DEGs, differentially expressed genes.

Figure 3 Heat map showing the expression pattern of 30 common DEGs in all tumor and normal samples.

Notes: The x-axis represents samples and y-axis represents genes. The bar on the top indicates the type of sample using red (tumor) and blue (normal).
Abbreviation: DEGs, differentially expressed genes.

Table 1 The identified 30 common DEGs in GSE46602 and GSE55945

Gene symbol	GSE46602		GSE55945
	Adjusted P-value	Log FC	Adjusted P-value	Log FC
ACSM1
AMACR	1.16E–05	2.88	0.00014732	3.22
AOC1	1.26E–09	−3.05	0.00356	−2.67
C1QTNF3-AMACR	9.23E–09	3.79	7.60E–06	3.38
CACNA1D	0.000226	2.08	5.58E–05	2.30
CCK	1.82E–07	−2.38	0.00125	−2.06
CD177	1.89E–12	−6.06	0.0298	−2.30
CYP3A5	1.31E–13	−3.73	0.001324667	−2.28
DLX1	3.35E–08	4.41	3.87E–08	4.16
DNAH5	2.61E–05	2.04	0.000519	2.04
F5	0.000165767	3.00	0.00329	2.16
HOXC4	1.51E–09	2.51	2.24E–06	2.56
HOXC6	2.91E–08	3.10	5.86E–07	3.33
HOXD10	8.37E–09	−2.30	0.00146	−2.05
HPN	2.97E–14	2.60	2.75E–07	2.36
INSM1	0.00204	2.15	0.000294	2.14
KCNG3	0.00233	2.06	0.0028	2.54
LINC00844	6.18E–12	−4.45	0.000129	−2.36
LOC100287413	1.58E–08	3.19	8.63E–08	2.40
LSAMP	5.33E–11	−2.75	6.56E–05	−2.10
MS4A8	0.000133	2.04	0.000398	2.82
OR51E2	0.0029	2.60	0.00765	2.26
PCA3	1.07E–06	4.19	4.70E–05	3.58
PDLIM5	1.41E–08	2.49	0.0004	2.36
PENK	2.25E–05	−2.26	8.98E–06	−2.39
PRCAT47	0.00012	3.07	5.97E–05	3.87
SIM2	3.80E–11	3.52	2.50E–05	2.10
SLC2A5	8.13E–11	−2.35	0.00025	−2.52
SV2B	6.19E–13	−3.16	0.000577	−2.30
TMEM45B	0.000505	2.42	0.001	2.49

Abbreviations: DEGs, differentially expressed genes; FC, fold change.

Table 2 KEGG pathway and GO enrichment results for the common DEGs

Type	ID	Term	Genes	P-value
KEGG	hsa04973	Carbohydrate digestion and absorption	SLC2A5, CACNA1D	0.0649
BP	GO:0006805	Xenobiotic metabolic process	CYP3A5, ACSM1, AOC1	0.0046
	GO:0009952	Anterior/posterior pattern specification	HOXC6, HOXC4, HOXD10	0.0049
	GO:0035641	Locomotory exploration behavior	PENK, LSAMP	0.0156
	GO:0009954	Proximal/distal pattern formation	DLX1, HOXD10	0.0310
	GO:0001662	Behavioral fear response	CCK, PENK	0.0373
CC	GO:0005886	Plasma membrane	HPN, SLC2A5, F5, PENK, CD177, LSAMP, SV2B, KCNG3, OR51E2, CACNA1D, AOC1	0.0387
MF	GO:0043565	Sequence-specific DNA binding	HOXC6, DLX1, HOXC4, HOXD10	0.0287
	GO:0003700	Transcription factor activity, sequence-specific DNA binding	HOXC6, INSM1, HOXC4, HOXD10, SIM2	0.0336
	GO:0005184	Neuropeptide hormone activity	CCK, PENK	0.0384

Abbreviations: BP, biological process; CC, cellular component; DEGs, differentially expressed genes; GEO, Gene Expression Omnibus; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function.

Figure 4 Regulation network between the identified common DEGs and reported miRNAs.

Note: Pink hexagons represent DEGs and green circles represent miRNAs.
Abbreviation: DEGs, differentially expressed genes.

Figure 5 Kaplan–Meier curves of GSE16560 dataset (A) and GSE40272 (B).

Notes: Censoring samples are marked with “+”. The x-axis represents time to event and y-axis represents percentage. The number of samples, censored number, and CI are shown in the insets. High- and low-risk groups are labeled with red and green curves, respectively. The red data represent high-risk patients, and the green data represent low-risk patients.
Abbreviation: CI, concordance index.

Table 3 Virtual validation results of prognostic performance

Dataset	Samples	Genes found	Risk groups (P-value)	DEGs between risk groups
				CI	DEGs (n)	DEGs
GSE16560	281	19	1.90E–07	66.6	9	CACNA1D, CCK, F5, HOXC4, HOXC6, LSAMP, MS4A7, PENK, SLC2A5
GSE40272	98	26	1.00E–05	89	6	CYP3A5, HOXC4, HOXC6, KCNG3, LSAMP, PENK

Abbreviations: CI, concordance index; DEGs, differentially expressed genes.