Bioinformatics-based study to detect chemical compounds that show potential as treatments for pulmonary thromboembolism

Abstract

The objectives of the present study comprised the recognition of major genes related to pulmonary thromboembolism (PTE) and the evaluation of their functional enrichment levels, in addition to the identification of small chemical molecules that may offer potential for use in PTE treatment. The RNA expression profiling of GSE84738 was obtained from the Gene Expression Omnibus database. Following data preprocessing, the differently expressed genes (DEGs) between the PTE group and the control group were identified using the Linear Models for Microarray package. Subsequently, the protein‑protein interaction (PPI) network of these DEGs was examined using the Search Tool for the Retrieval of Interacting Genes/Proteins database, visualized via Cytoscape. The most significantly clustered modules in the network were identified using Multi Contrast Delayed Enhancement, a plugin of Cytoscape. Subsequently, functional enrichment analysis of the DEGs was performed, using the Database for Annotation Visualization and Integrated Discovery tool. Furthermore, the chemical-target interaction networks were investigated using the Comparative Toxicogenomics Database as visualized via Cytoscape. A total of 548 DEGs (262 upregulated and 286 downregulated) were identified in the PTE group, compared with the control group. The upregulated and downregulated genes were enriched in Gene Ontology terms related to inflammation and eye sarco-lemma, respectively. Tumor necrosis factor (TNF) and erb-b2 receptor tyrosine kinase 2 (ERBB2) were upregulated genes that ranked higher in the PPI network (47 and 40 degrees, respectively) whereas C‑JUN was the most downregulated gene (46). Small chemical molecules ethinyl (135), cyclosporine (126), thrombomodulin precursor (113) and tretinoin (111) had >100 degrees in the DEG‑chemical interaction network. In addition, ethinyl targeted to TNF, whereas TNF and ERBB2 were targeted by cyclosporine, and tretinoin was a targeted chemical of ERBB2. Therefore, cyclosporine, ethinyl, and tretinoin may be potential targets for PTE treatment.

Clinical Characteristics of Patients with Pulmonary Thromboembolism Based on Computer Statistical Analysis

“…PE has a high rate of misdiagnosis, missed diagnosis, and mortality in clinical practice. The first venous thromboembolism (VTE) in the United States every year is 100/100,000, of which about 30% develop into PE [ 5 ]. Foreign autopsy statistics have found that the missed diagnosis rate of pulmonary embolism is as high as 67%, and the misdiagnosis rate is as high as 63%.…”

Integrated bioinformatics analysis of core regulatory elements involved in keloid formation

“…Search Tool for the Retrieval of Interacting Genes/Proteins (STRING; http://string-db.org/ ) was used to construct interaction networks among the DEGs-coded proteins(setting criteria: medium confidence ≥ 0.9) [ 13 ]. The most significant PPIs were plotted with the application of Cytoscape (v3.7.2, http://cytoscape.org/ ) [ 14 ] and the top module with the highest score (setting: k-core > 2) was identified. The proteins encoded by genes in the same module tended to have the same or analogous functions, and these proteins were enriched for the same biological role [ 15 ].…”

Lateral rectus muscle differentiation potential in paralytic esotropia patients

“…If one gene was detected by multiple probes, the mean value of the probes can then represent the expression level [ 7 ]. Gene expression data from the paralytic and concomitant esotropia groups were separated according to the Linear Models for Microarray Data package (LIMMA), and DEGs between the two groups were screened in R software [ 8 ].…”