Identification of potential biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma by bioinformatics analysis

Figures & data

Table 1 Functional and pathway enrichment analysis of upregulated and downregulated DEGs in HNSCC

ID	Go term	Count	P-value
GO_function
GO_BP:0030198	ECM organization	43	2.07E–18
GO_BP:0002479	Antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	23	5.77E–15
GO_BP:0030574	Collagen catabolic process	21	1.10E–12
GO_BP:0060337	Type I interferon signaling pathway	20	1.13E–11
GO_BP:0031145	Anaphase-promoting complex-dependent catabolic process	21	8.10E–11
GO_CC:0070062	Extracellular exosome	213	2.62E–20
GO_CC:0005576	Extracellular region	129	1.88E–13
GO_CC:0005615	Extracellular space	113	4.42E–13
GO_CC:0005578	Proteinaceous ECM	41	1.51E–12
GO_CC:0031012	ECM	43	2.31E–12
GO_MF:0004298	Threonine-type endopeptidase activity	11	4.09E–09
GO_MF:0005201	ECM structural constituent	17	1.38E–08
GO_MF:0005518	Collagen binding	14	1.05E–06
GO_MF:0004252	Serine-type endopeptidase activity	28	1.18E–05
GO_MF:0005515	Protein binding	429	1.27E–05
KEGG_PATHWAY
Hsa:04512	ECM–receptor interaction	23	1.23E–10
Hsa:05146	Amebiasis	25	2.11E–10
Hsa:03050	Proteasome	15	1.25E–08
Hsa:04510	Focal adhesion	30	2.76E–07
Hsa:05222	Small cell lung cancer	16	1.52E–05

Note: Top five terms were selected according to P-value.

Abbreviations: DEGs, differentially expressed genes; HNSCC, head and neck squamous cell carcinoma; GO, gene ontology; BP, biological process; ECM, extracellular matrix; MHC, major histocompatibility; TAP, transporter associated with antigen processing; CC, cellular component; MF, molecular function.

Figure 1 PPI network of differentially expressed genes.

Notes: Blue represents downregulated DEGs; red represents upregulated DEGs.
Abbreviations: PPI, protein–protein interaction; DEGs, differentially expressed genes.

Figure 2 Functional modules in the PPI network.

Notes: From PPI networks of DEGs with combined score >0.8, we clustered two functional modules, using MCODE: module 1 (A) and module 2 (B). Blue represents downregulated DEGs; red represents upregulated DEGs.
Abbreviations: PPI, protein–protein interaction; DEGs, differentially expressed genes; MCODE, Molecular Complex Detection.

Table 2 The hub genes that had a degree >22 in PPI network

Gene	Regulation	Degree
CDK1	Up	36
PTK2	Up	34
ITGAV	Up	29
APP	Up	28
COL1A1	Up	27
MMP9	Up	27
AURKA	Up	26
BMP2	Up	26
ITGB4	Up	26
CDC20	Up	25
SDC4	Up	25
COL1A2	Up	23
ITGA6	Up	23
PSMA7	Up	23
STAT1	Up	23

Abbreviation: PPI, protein–protein interaction.

Table 3 Functional and pathway enrichment analysis of the DEGs in modules

ID	Description	Count	P-value
Module 1
GO_BP:0031145	Anaphase-promoting complex-dependent catabolic process	17	1.73E–36
GO_BP:0051436	Negative regulation of ubiquitin protein ligase activity involved in mitotic cell cycle	16	4.09E–34
GO_BP:0051437	Positive regulation of ubiquitin protein ligase activity involved in regulation of mitotic cell cycle transition	16	1.27E–33
GO_BP:0006521	Regulation of cellular amino acid metabolic process	14	2.99E–30
GO_BP:0043161	Proteasome-mediated ubiquitin-dependent protein catabolic process	16	8.04E–27
GO_CC:0000502	Proteasome complex	12	5.82E–24
GO_CC:0005839	Proteasome core complex	8	2.77E–17
GO_CC:0005829	Cytosol	19	4.58E–14
GO_CC:0005654	Nucleoplasm	16	2.87E–10
GO_CC:0005634	Nucleus	18	1.40E–08
GO_MF:0004298	Threonine-type endopeptidase activity	8	2.90E–17
GO_MF:0005515	Protein binding	18	1.49E–05
Hsa:03050	Proteasome	12	2.16E–21
Module 2
GO_BP:0030198	ECM organization	17	5.98E–29
GO_BP:0030574	Collagen catabolic process	12	7.33E–23
GO_BP:0030199	Collagen fibril organization	7	2.78E–12
GO_BP:0071230	Cellular response to amino acid stimulus	7	9.11E–12
GO_BP:0007155	Cell adhesion	9	1.70E–08
GO_CC:0005788	Endoplasmic reticulum lumen	15	1.42E–24
GO_CC:0005581	Collagen trimer	11	5.76E–19
GO_CC:0005576	Extracellular region	15	1.27E–11
GO_CC:0031012	ECM	9	2.85E–10
GO_CC:0005578	Proteinaceous ECM	8	5.96E–09
GO_MF:0005201	ECM structural constituent	11	4.30E–20
GO_MF:0048407	Platelet-derived growth factor binding	5	3.76E–10
GO_MF:0038132	Neuregulin binding	3	1.20E–05
Hsa:04512	ECM–receptor interaction	15	5.56E–25
Hsa:04974	Protein digestion and absorption	13	4.91E–20
Hsa:04510	Focal adhesion	15	1.76E–19
Hsa:05146	Amebiasis	12	7.43E–17
Hsa:04151	PI3K-Akt signaling pathway	15	2.72E–16
Hsa:05222	Small cell lung cancer	7	3.22E–08

Abbreviations: DEGs, differentially expressed genes; GO, gene ontology; BP, biological process; MHC, major histocompatibility; TAP, transporter associated with antigen processing; CC, cellular component; ECM, extracellular matrix; MF, molecular function.

Figure 3 Kaplan–Meier curves depicting OS in the TCGA HNSCC cohort with high and low expression of PMSA7 (A), ITGA6 (B), ITGB4 (C) and APP (D), respectively. Abbreviations: OS, overall survival; HNSCC, head and neck squamous cell carcinoma; HR, hazard ratio; CI, confidence interval.