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Bioinformatics analysis of key genes in patients with sarcoidosis and prediction of traditional Chinese Medicine

Published: 31 May 2023 Publication History

Abstract

Bioinformatics methods were used to analyze the key genes and related signal paths of sarcoidosis. RNA-seq of sarcoidosis were downloaded from the gene expression omnibus (GEO) database (GSE42826 and GSE42830) and differentially expressed genes (DEGs) were extracted from the two chip datasets. We uesd the gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO) way to analyse DEGs, the cytoscape 3.8.2 softwarethe was uesd to visualize the DEGs. The ggpubr package was used to draw the volcano map of DEGs. Ggplot package to draw bubble charts for GO, KEGG, DO analysis. PPI analysis was used to identified hub genes, hub genes were verified in the GSE19314 dataset. 64 DEGs were obtained in the GSE42826 and GSE42830 datasets, of which 17 genes were down-regulated genes and 47 genes were up-regulated genes. GO analysis indicated that DEGs were mainly enriched in external stimuli, defense responses, and responses to biological stimuli in other biological processes, KEGG analysis showed that DEGs mainly affect NOD-like receptor signaling pathways, programmed pell death-ligand 1(PD-L1) expression, programmeddeath-1(PD-1) checkpoint pathways in cancer and cytoplasmic deoxyribonucleic acid (DNA) sensing pathways. The results of DO analysis showed that DEGs were associated with bacterial infectious diseases, hepatitis, primary bacterial infectious diseases. 8 hub genes, including C-X-C motif chemokine ligand 10 (CXCL10), interferon induced protein 44 (IFI44) and interferon induced protein with tetratricopeptide repeats 3 (IFIT3), were all significantly up-regulated in sarcoidosis group. Further analysis showed that sarcoidosis was sensitive to pinellia, radix isatidis, ephedra and phellodendri. This work showed that 10 hub genes may become relevant targets for diagnosis and treatment of patients with sarcoidosis and provided a new idea for the pathogenesis and treatment of sarcoidosis.

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BIC '23: Proceedings of the 2023 3rd International Conference on Bioinformatics and Intelligent Computing
February 2023
398 pages
ISBN:9798400700200
DOI:10.1145/3592686
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

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Published: 31 May 2023

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