Resultsįunctional and pathway enrichment analysis demonstrated that the upregulated differentially expressed genes (DEGs) were significantly enriched in CXCR chemokine receptor binding, chemokine activity, chemokine receptor binding, G-protein coupled receptor binding, RAGE receptor binding, cytokine activity, microtubule binding, receptor regulator activity and microtubule motor activity, and the down-regulated genes were highly enriched in collagen binding. Gene set enrichment analysis (GSEA) and mutation analysis were also performed for hub genes. And then we did ROC curve analysis by SPSS. We validated the key genes in TCGA, GEPIA, UALCAN and Immunohistochemistry staining obtained from The Human Protein Atlas database. The Venn diagram was performed to overlap the gene in key module and hub PPI cluster. Next, we utilized the “WGCNA” package in R to establish co-expression network for the DEGs. We also performed functional analysis on the genes in the hub module by using clusterprofiler. We utilized Search Tool for the Retrieval of Interacting Genes Database (STRING) to assess protein–protein interaction (PPI) information, and then we used plug-in Molecular Complex Detection (MCODE) to screen hub modules of PPI network in Cytoscape. Enrichment of the functions and pathways was analyzed by using clusterprofiler. We performed the “limma” R language package to screen DEGs between Endometrial cancer tissue samples and normal uterus tissue samples. Calculate raw expression data according to pre-processing procedures. Methodsĭownload the gene expression profile from Gene Expression Omnibus (GEO). Bioinformatics analysis has been widely applied to screen and analyze genes in linkage to various types of cancer progression. Endometrial cancer predominately affects post-menopausal women. This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.Endometrial cancer (EC) is one of the female malignant tumors. The hub node STAT1 in PPI networks and TF network may be specifically involved in pathogenic mechanisms of FK. In the current study, our results revealed key elements and their interactions involved in FK. Additionally, using Enrichr, the TF network was established, in which the top five TF STAT1, SMAD3, FOS, NOD2, and YAP1. Module analysis revealed that FK was significantly associated with immune response, such as chemokine signaling pathway, Antigen processing and presentation, and cell adhesion molecules (CAMs). A total of 838 nodes interacted with each other in PPI networks, including top 10 hub genes SRC, SYK, TNF, VEGFA, IL8, STAT1, MAPK1, VCAM1, CSF2, EGFR, and RAC2. GO and KEGG pathway analysis showed that the up-regulated DEGs were mainly enriched in function of neutrophil and leukocyte, ERK1 and ERK2 cascade, and chemokine signaling pathway, while the down-regulated DEGs were mainly involved in BMP signal pathway and glycine, serine and threonine metabolism. Transcription factors (TF) in DEGs were obtained from Enrichr, which network was constructed using Cytoscape software.Ī total of 896 upregulated genes and 570 downregulated genes in FK were identified. Cytoscape software was used to screen the hub genes and constructed modules of PPI network were identified. STRING database was used to constructed the protein-protein interaction (PPI) networks of the DEGs. Gene ontology (GO) and KEGG pathway enrichment analyses were performed using R packages Clusterprofiler. Differentially expressed genes (DEGs) between FK and NC samples were identified by GEO2R. The expression profiles of GSE58291 were downloaded from the Gene Expression Omnibus (GEO) database, including 12 normal corneal (NC) tissues and 5 keratitis subjects with culture positive for Fusarium sp. In this study, integrative bioinformatics approach for transcriptomic data was used to screen and verify key elements and hub genes involved in Fusarium sp.-associated keratitis (FK) and explore potential molecular mechanisms. and Aspergillus flavus with different microbiological characteristics and host immune responses. Fungal keratitis is a devastating ulcerative corneal infection causing by two primary pathogenic fungi Fusarium sp.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |