Identification of potential hub genes and therapeutic drugs in ovarian cancer via bioinformatics analysis

Figures & data

Figure 1. Identification of ovarian cancer (OC)-related differentially expressed genes (DEGs). (A) Volcano plots of DEGs between tumor and normal samples. Blue represents downregulated DEGs, red represents upregulated DEGs. (B) Venn diagram of the DEGs and ovarian disease-related genes.

Figure 2. Functional enrichment analysis of DEGs. (A) Top 20 enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. (B) Network of enriched GO terms and KEGG pathways. Different node colors indicate different clusters, and the lines indicate similarities among genes annotated with each term.

Figure 3. Protein-protein interaction (PPI) network. Different colors indicate the different modules identified using Molecular Complex Detection (MCODE). Triangles and inverted triangles indicate the upregulated and downregulated genes, respectively. Node size indicates the degree of connectivity, and gray lines represent interactions between proteins.

Table 1. The GO-BP function and KEGG pathway of DEGs in 10 modules extracted from PPI network.

Modules	GO	Description	Count	Log10(P)
Module 1	GO:0070098	Chemokine-mediated signaling pathway	13	−28.7
Module 1	GO:1990869	Cellular response to chemokine	13	−28.1
Module 1	GO:1990868	Response to chemokine	13	−28.1
Module 2	GO:0051301	Cell division	15	−24.2
Module 2	GO:0000070	Mitotic sister chromatid segregation	11	−21.2
Module 2	GO:0140014	Mitotic nuclear division	12	−20.9
Module 3	GO:2001022	Positive regulation of response to DNA damage stimulus	4	−7.3
Module 3	GO:2001020	Regulation of response to DNA damage stimulus	4	−5.9
Module 3	GO:0051054	Positive regulation of DNA metabolic process	4	−5.8
Module 4	GO:0051321	Meiotic cell cycle	5	−8.2
Module 4	hsa04110	Cell cycle	4	−7.3
Module 4	hsa05200	Pathways in cancer	5	−7.2
Module 5	GO:0043966	Histone H3 acetylation	3	−6
Module 5	GO:0007098	Centrosome cycle	3	−5.1
Module 5	GO:0031023	Microtubule organizing center organization	3	−5
Module 6	GO:0038128	ERBB2 signaling pathway	3	−7.1
Module 6	GO:0097191	Extrinsic apoptotic signaling pathway	4	−6.6
Module 6	GO:0038034	Signal transduction in absence of ligand	3	−6.1
Module 7	GO:0090068	Positive regulation of cell cycle process	5	−8.8
Module 7	GO:0045787	Positive regulation of cell cycle	5	−8.2
Module 7	hsa04110	Cell cycle	4	−8
Module 8	GO:0018108	Peptidyl-tyrosine phosphorylation	5	−8.3
Module 8	GO:0018212	Peptidyl-tyrosine modification	5	−8.3
Module 8	GO:0030335	Positive regulation of cell migration	5	−7.5
Module 9	GO:0010389	Regulation of G2/M transition of mitotic cell cycle	3	−6.3
Module 9	GO:1902749	Regulation of cell cycle G2/M phase transition	3	−6.2
Module 9	GO:0000086	G2/M transition of mitotic cell cycle	3	−6
Module 10	hsa05205	Proteoglycans in cancer	3	−6.2
Module 10	GO:0030198	Extracellular matrix organization	3	−5.4
Module 10	GO:0043062	Extracellular structure organization	3	−5.3

Notes: GO-BP, Gene Ontology-biological process; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEGs, differentially expressed genes; PPI, protein-protein interaction network.

Figure 4. Gene-drug interaction network (A) and drug-pathway network (B). (A) Red triangles indicate upregulated genes; green inverted triangles indicate downregulated genes; gray rectangles indicate predicted drugs. (B) Yellow squares indicate KEGG pathways and white squares indicate predicted drugs.

Figure 5. Survival analysis of key genes in OC using Kaplan – Meier analysis. (A) CCND1, (B) CCNE1, (C) CXCL10, (D) ERBB4, (E) LPAR3, (F) SST, (G) ERBB4, and (H) LPAR3. Patients were split into high and low expression groups based on the median expression of genes.

Figure 6. Protein expression of key genes verified using the Human Protein Atlas (HPA) database. (A) AURKB, (B) CENPE, (C) DCN, (D) LYN, (E) PDGFRA, and (F) PDGFRB.

Figure 7. Validation of key genes using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Data are presented as mean ± standard deviation. Statistical significance was determined using two-tailed t-test; * P < 0.05; *** P < 0.001.

Data availability statement

The data were derived from the following resources available in the public domain: the UCSC Xena database (https://xena.ucsc.edu/), GENCODE database (https://www.gencodegenes.org/), and DISEASES (https://diseases.jensenlab.org/Search). The qRT-PCR data in this study are available in 4TU. ResearchData under DOI: https://doi.org/10.4121/22267030 at https://doi.org/10.4121/22267030.