Fig 1.
B Analysis of COPD differentially expressed genes (DEGs) in comparison to corresponding controls (A) Volcano plots of log fold changes in gene expression. (B) Identification of 63 common DEGs from blood and lung tissue datasets using VENNY. The overlapped area defines the shared DEGs of lung tissue and blood. (C) Heatmap of DEGs with a LogFC > 1.5. Red: up-regulation; green: down-regulation.
Fig 2.
Hub genes TMEM67, IRAK2, ASB4, MECOM, DPF3 and DDX3Y with their clusters identified from the common DEGs between blood and lung tissue datasets.
Their selection is based on degree of centrality in the PPI network with the score >18.
Table 1.
A total of 12 significant genes with more than 17 of DC were obtained from network analysis and chosen as hub proteins.
Fig 3.
GO-annotations stacked network view of (A) MECOM and (B) IRAK2 clusters. The size of the circle (left side) represents the number of genes involved in a specific GO-term. The GWAS loci of (C) MECOM (D) IRAK2 genes from the GWAS catalog.
Table 2.
Functional enrichment of CCDC74B, MECOM, IRAK2 and DET1 clusters, in which highlights highest functional enrichment in different molecular processes like molecular function (MF), biological process (BP), cellular components (CC) and KEGG pathways based on FDR value.
Fig 4.
Expression levels in lung adenocarcinoma and lung squamous cell carcinoma cells in compression to normal tissues from GEPIA2.
A) SREK1. B) IRAK2. C) DDX3Y. D) C1QTNF2. The signature score is calculated by mean value of log2 (TPM + 1). The |Log2FC| cutoff of the expression of proposed biomarker was 1. The p-value cutoff of the expression of proposed biomarker was 0.01. The red box indicates the tumor samples while the gray one represents the normal tissues. E. Pathological Stage Plot of SREK1, IRAK2, DDX3Y and C1QTNF2 genes in lung cancer.
Table 3.
Association of two hub genes with the lung related traits and lung cancer from GWAS catalog database.
Fig 5.
The prognostic values (patient survival in days) of the expression status of 6 COPD-hub genes.
A) SREK1 (P<0.001). B) TMEM67 (P = 0.002). C) CDC42BPA (P = 0.003). D) DPF3 (P = 0.005). E) ASB4 (P = 0.024) F) IRAK2 (P = 0106). The correlation of survival status of patients with different lung cancer subtypes (Squamous, Adeno, Large) to all six genes expression level.
Fig 6.
The expression of the two hub genes from the Human Protein Atlas (HPA) in normal and cancer lung tissue.
Table 4.
The expression levels of the 10 hub genes in normal lung and cancer tissues: Human Protein Atlas (HPA).