20 hours ago · Hub Gene Selection. The plug-in CytoHubba (version 1.6) in Cytoscape was used to explore significant genes in the PPI network, and the genes with most interactions were referred as hub genes, which might play core roles in the disease pathogenesis. 17 We used Maximal Clique Centrality (MCC) to calculate the hub genes. >> Go To The Portal
The transcription factors of hub genes. A red node indicates the hub gene and a gray node indicates the transcription factor. Table 2 Transcription factor analysis of key differentially expressed genes. TFs Genes
Functional modules and hub genes were screened by MCODE and cytohubba plug-ins, and the Cancer Genome Atlas (TCGA) survival analysis and qRT-PCR were utilized to validate the expression of these hub genes on TNBC. Results A total of 134 DEGs were identified by differential expression analysis, consisting of 88 up- and 46 down-regulated genes.
In the current study, we also identified a number of TFs that have close interactions with the hub DEGs. Interferon regulatory factor 1 (IRF1) is a member of a family of transcription factors that regulates the expression of interferons. It is believed that the IFN system plays a key role in the pathogenesis of SLE.
We used the GEO2R tool to identify the differentially expressed genes (DEGs) in SLE-related datasets retrieved from the Gene Expression Omnibus (GEO). In addition, we also identified the biological functions of the DEGs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis.
According to the existing studies, the hub genes play key roles in multiple cancer-related biological processes. CD3D, CD3Eand CD3Gare located in the same cluster on chromosome 11, and encode a group of polypeptide named CD3-delta, CD3-gamma and CD3 epsilon.
Triple negative breast cancer (TNBC) is an intrinsic subtype of breast cancer with a poor prognosis, character ized by a lack of ER and PR expression and the absence of HER2 amplification.