Identification of potential core genes in triple negative breast cancer using bioinformatics analysis

Figures & data

Table 1 Statistics of the three microarray databases derived from the GEO database

Dataset ID	TNBC	Normal	Total number
GSE38959	30	13	43
GSE45827	41	11	52
GSE65194	41	11	52

Abbreviations: GEO, Gene Expression Omnibus; TNBC, triple-negative breast cancer.

Figure 1 Venn diagram of DEGs common to all three GEO datasets.

Notes: (A) Downregulated genes. (B) Upregulated genes.
Abbreviations: DEG, differentially expressed gene; GEO, Gene Expression Omnibus.

Table 2 Significantly enriched GO terms and KEGG pathways of DEGs

Category	Term	Description	Count	P-value
BP term	GO:0007062	Sister chromatid cohesion	23	4.30E–15
BP term	GO:0007018	Microtubule-based movement	11	2.59E–05
BP term	GO:0031145	Anaphase-promoting complex-dependent catabolic process	10	1.24E–04
BP term	GO:0030198	ECM organization	14	1.03E–03
CC term	GO:0000777	Condensed chromosome kinetochore	23	6.49E–17
CC term	GO:0000776	Kinetochore	17	7.09E–11
CC term	GO:0005819	Spindle	14	6.63E–06
CC term	GO:0005874	Microtubule	19	5.31E–04
MF term	GO:0008017	Microtubule binding	20	7.71E–07
MF term	GO:0003777	Microtubule motor activity	11	2.27E–05
MF term	GO:0001077	Transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	15	1.90E–03
MF term	GO:0016887	ATPase activity	12	5.11E–03
KEGG pathway	hsa05222	Small cell lung cancer	11	1.76E–04
KEGG pathway	hsa05200	Pathways in cancer	26	1.95E–04
KEGG pathway	hsa04512	ECM–receptor interaction	11	2.14E–04

Abbreviations: BP, biological process; CC, cellular component; DEG, differentially expressed gene; ECM, extracellular matrix; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function.

Table 3 Top ten hub genes with higher degree of connectivity

Gene symbol	Gene description	Degree
CDK1	Cyclin-dependent kinases 1	64
CCNB1	Cyclin B1	61
BIRC5	Baculoviral IAP repeat containing 5	60
AURKA	Aurora kinase A	58
PLK1	Polo-like kinase 1	56
MAD2L1	Mitotic arrest deficient 2-like 1	54
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	54
NDC80	Nuclear division cycle 80	53
BUB1	Budding uninhibited by benzimidazoles 1	52
KIF11	Kinesin family member 11	52

Figure 2 Protein–protein interaction network constructed with the differentially expressed genes.

Note: Red nodes represent upregulated genes, and blue nodes represent downregulated genes.

Figure 3 Kaplan–Meier overall survival analyses for the top ten hub genes expressed in breast cancer patients.

Note: See Table 3 for gene description.

Figure 4 Kaplan–Meier relapse-free survival analyses for CCNB1 expression in TNBC patients.

Abbreviations: CCNB1 cyclin B1; TNBC, triple-negative breast cancer.

Table S1 The desired probes of hub genes in the Kaplan–Meier plotter database

Gene symbol	Probe ID
CDK1	203213_at
CCNB1	228729_at
BIRC5	202094_at
AURKA	208079_s_at
PLK1	202240_at
MAD2L1	203362_s_at
BUB1B	203755_at
NDC80	204162_at
BUB1	209642_at
KIF11	204444_at