Abstract
Background Tuberculosis (TB) is usually caused by Mycobacterium tuberculosis, which has the highest mortality rate among infectious diseases. This study is designed to identify the key genes affecting the diagnosis and treatment of TB. Methods GSE54992, which included 39 peripheral blood mononuclear cell (PBMC) samples, was extracted from the Gene Expression Omnibus database. After the samples were classified into type and time groups by limma package, the differentially expressed genes (DEGs) were analyzed using the Analysis of Variance. Using pheatmap package, hierarchical cluster analysis was performed for the DEGs. Then, the key modules correlated with TB were selected using the WGCNA package. Finally, functional and pathway enrichment analyses were carried out using clusterProfiler package. Results The DEGs in subclusters 3, 6, 7, and 8 were chosen for further analyses. Based on WGCNA analysis, blue and green modules in type group and pink module in time group were selected as key modules. From the key modules, 9 (including BAX and ARPC1B) hub genes in type group and 6 (including DHX36) hub genes in time group were screened. Through pathway enrichment analysis, the TNF signaling pathway was enriched for the green module. Conclusion DHX36, BAX, and ARPC1B might be key genes acting in the mechanisms of TB. Besides, the TNF signaling pathway might also be critical for the diagnosis and therapy of the disease.
Highlights
IntroductionTuberculosis (TB) is mainly induced by Mycobacterium tuberculosis (MTB) and usually affects the lungs [1, 2]
As an infectious disease, tuberculosis (TB) is mainly induced by Mycobacterium tuberculosis (MTB) and usually affects the lungs [1, 2]
A total of 462, 1502, and 741 differentially expressed genes (DEGs) separately were screened in TB3m vs. TB, TB6m vs. TB, and TB6m vs. TB3m time comparison groups (Table 1). e cluster heatmap for all DEGs showed that the DEGs could separate the samples in different groups very well (Figure 2)
Summary
Tuberculosis (TB) is mainly induced by Mycobacterium tuberculosis (MTB) and usually affects the lungs [1, 2]. Tuberculosis (TB) is usually caused by Mycobacterium tuberculosis, which has the highest mortality rate among infectious diseases. Is study is designed to identify the key genes affecting the diagnosis and treatment of TB. After the samples were classified into type and time groups by limma package, the differentially expressed genes (DEGs) were analyzed using the Analysis of Variance. Based on WGCNA analysis, blue and green modules in type group and pink module in time group were selected as key modules. 9 (including BAX and ARPC1B) hub genes in type group and 6 (including DHX36) hub genes in time group were screened. The TNF signaling pathway might be critical for the diagnosis and therapy of the disease
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