Identification of key genes for type 1 diabetes mellitus by network-based guilt by association

Abstract

SUMMARY OBJECTIVE This study aimed to propose a co-expression-network (CEN) based gene functional inference by extending the “Guilt by Association” (GBA) principle to predict candidate gene functions for type 1 diabetes mellitus (T1DM). METHODS Firstly, transcriptome data of T1DM were retrieved from the genomics data repository for differentially expressed gene (DEGs) analysis, and a weighted differential CEN was generated. The area under the receiver operating characteristics curve (AUC) was chosen to determine the performance metric for each Gene Ontology (GO) term. Differential expression analysis identified 325 DEGs in T1DM, and co-expression analysis generated a differential CEN of edge weight > 0.8. RESULTS A total of 282 GO annotations with DEGs > 20 remained for functional inference. By calculating the multifunctionality score of genes, gene function inference was performed to identify the optimal gene functions for T1DM based on the optimal ranking gene list. Considering an AUC > 0.7, six optimal gene functions for T1DM were identified, such as regulation of immune system process and receptor activity. CONCLUSIONS CEN-based gene functional inference by extending the GBA principle predicted 6 optimal gene functions for T1DM. The results may be potential paths for therapeutic or preventive treatments of T1DM.

The relationship between plasma serglycin levels and the diagnosis of diabetic retinopathy

“…Recently, several genes have been identified as having a potential diagnostic and prognostic value in DM and related complications such as diabetic nephropathy and diabetic cardiomyopathy. [12][13][14] In the realm of DR, various genes were also found to be potential candidates for DR diagnosis and progression. For instance, Li et al found that angiogenesis growth factors VEGFC, ANGPT1, ANGPT2, and EFNB2 were upregulated in DR patients, presenting their potentials as biomarkers for DR diagnosis and treatment.…”