Identification of hub genes with prognostic values in multiple myeloma by bioinformatics analysis

Figures & data

Figure 1. Identification of differentially expressed genes in two GE profiles (GSE80140 and GSE80545). (a) Respective volcanic maps of the two datasets. Up (red plots), the expression is up-regulated; down (green plots), the expression is down-regulated; no (gray plots), no significantly dysregulated. (b) Heatmaps of top 50 dramatically altered genes of DEGs in GSE80140 and GSE80545. (C) Commonly changed DEGs in the two datasets (119 up – and 67 down-regulated genes). DEGs, differentially expressed genes.

Figure 2. GO and KEGG enrichment analysis of DEGs. (a) GO analysis including BP, MF, and CC three subontologies. (b) KEGG pathway enrichment analysis. GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEGs, differentially expressed genes; BP, biological process; MF, molecular function; CC, cellular component.

Table 1. Top 5 enriched terms of GO analysis.

Term	Description	Count	p-value
BP
GO:0036123	Histone H3-K9 dimethylation	3	1.78E-04
GO:0006418	tRNA aminoacylation for protein translation	5	2.53E-04
GO:0043276	Anoikis	3	3.53E-04
GO:0006260	DNA replication	7	0.001308
GO:0006520	Cellular amino acid metabolic process	4	0.003634
MF
GO:0003824	Catalytic activity	21	6.95E-04
GO:0044822	Poly(A) RNA binding	8	4.81E-04
GO:0005524	ATP binding	20	0.023579
GO:0005515	Protein binding	81	0.028966
GO:0003873	Phosphofructo-2-kinase activity	2	0.030916
CC
GO:0005654	Nucleoplasm	42	5.47E-06
GO:0005739	Mitochondrion	26	1.20E-05
GO:0005743	Mitochondrial inner membrane	12	4.19E-04
GO:0005829	Cytosol	40	0.001316
GO:0005730	Nucleolus	16	0.001598

Table 2. DEGs identified from GO and KEGG analysis.

DEGs	Gene names
GO enrichment analysis	KDM3A, SUV39H2, SUV39H1, PFKFB3, NTHL1, MRTO4, CSTF2, DDX39A, PAK1IP1, ASF1B, FKBP4, UBE2T, HNRNPAB, POP1, KDM4B, ORC6, UTP20, FEN1, CDC6, MRPS26, GAR1, TIPIN, MAFF, PNPO, RNASEH2A, RTEL1, BANF1, CAD, PSMG1, RRP9, E2F1, MPHOSPH6, KPNA2, GMNN, METTL1, POLR3G, SNRNP25, SNRPD1, WDR77, POLR3 K, TIMM50, CDC25A, FH, FLAD1, PFKFB4, ISOC2, TSTA3, SCLY
KEGG pathway enrichment analysis	TSTA3, FH, GAL3ST1, PYCRL, ATP8, ATP5G1, HSD17B10, HK2, SRM, GCSH, IL4I1, FLAD1, PNPO, SEPHS1, GGT6, CAD, GOT2, COQ3, P4HA1, MTHFD1, NDUFS6, POLR3G, SCLY, POLR3K, DCTPP1

Figure 3. PPI network analysis. (a, b) The PPI analysis at STRING. (c, d) Cytoscape plug-ins cytoHubba analysis of candidate genes after PPI analysis. (a, c) Genes identified from GO analysis. (c, d) Genes identified from KEGG analysis. PPI, protein–protein interaction.

Table 3. The genes with the score of each analysis through the Cytoscape ‘cytoHubba’ module analysis

GO analysis						KEGG analysis
Rank	Name	Score	Rank	Name	Score	Rank	Name	Score
1	FEN1	112	23	KDM4B	4	1	GOT2	4
2	CDC6	108	24	UTP20	4	2	FH	3
3	GMNN	72	25	SUV39H1	4	3	ATP5G1	3
4	TIPIN	54	26	NTHL1	4	4	TSTA3	2
5	CDC25A	36	27	SNRNP25	3	5	POLR3K	2
6	ASF1B	32	28	FH	3	6	HK2	2
7	UBE2T	30	29	PFKFB3	2	7	SRM	2
8	ORC6	30	30	RTEL1	2	8	CAD	2
9	KPNA2	27	31	POLR3K	2	9	PNPO	2
10	RRP9	22	32	POP1	2	10	IL4I1	2
11	SNRPD1	17	33	SUV39H2	2	11	PYCRL	2
12	RNASEH2A	17	34	MPHOSPH6	2	12	GCSH	2
13	HNRNPAB	14	35	TSTA3	1	13	MTHFD1	1
14	DDX39A	14	36	PFKFB4	1	14	GGT6	1
15	MRTO4	14	37	POLR3G	1	15	DCTPP1	1
16	CSTF2	12	38	ISOC2	1	16	POLR3G	1
17	GAR1	10	39	PNPO	1	17	NDUFS6	1
18	E2F1	8				18	SEPHS1	1
19	METTL1	7				19	SCLY	1
20	WDR77	6				20	COQ3	1
21	PAK1IP1	6				21	MT-ATP8	1
22	KDM3A	5				22	P4HA1	1

Figure 4. Correlation between individual statistically significant DEG expression and DSS in MM. Kaplan–Meier survival curves comparing high and low expression of DEGs in MM in PrognoScan, as based on the GSE2658 dataset (n = 559). Cox p < 0.05 was considered as statistically significant. DEGs, differentially expressed genes; DSS, disease-specific survival; MM, multiple myeloma.