Latent Pathways Identification by Microarray Expression Profiles in Thyroid-Associated Ophthalmopathy Patients

This study aimed to screen potential genes related to thyroid-associated ophthalmopathy (TAO) and get a further understanding about the pathogenesis of this disease. GSE9340 was downloaded from Gene Expression Omnibus, including eight thyroid tissue samples from hyperthyroid patients without TAO and ten ones from hyperthyroid patients with TAO. The differentially expressed genes (DEGs) were identified by the linear models for microarray data package. And their potential functions were predicted by Gene Ontology (GO) and pathway enrichment analyses. Furthermore, protein-protein interaction (PPI) was obtained from the Search Tool for the Retrieval of Interacting Genes database, and the PPI network was visualized with Cytoscape. Then, module analysis was performed by the Molecular Complex Detection analysis. Additionally, the potential pathway interactions were identified by Latent Pathway Identification Analysis. Totally, 511 upregulated and 507 downregulated DEGs in TAO were screened. Some DEGs (e.g., UBE2C) were related to cell cycle, and DEGs encoding proteasome (e.g., PSMA1, PSMC5, PSMC4, and PSMD1) were related to negative regulation of ubiquitin-protein ligase activity. Several upregulated DEGs encoding signal recognition particle (e.g., SRP14, SRP54, and SRP9) were found to be enriched in protein export pathway. Furthermore, some pathways (e.g., ribosome and protein export) had interactions. The DEGs related to cell cycle (e.g., UBE2C), DEGs encoding proteasome (e.g., PSMA1, PSMC5, PSMC4, and PSMD1) and signal recognition particle (e.g., SRP14, SRP54, and SRP9), as well as pathways of ribosome, protein export and retinol metabolism, might play key roles in the development of TAO.