We screened for differentially expressed proteins (DEPs) associated with autophagy by limma package in R. For the genes corresponding to the DEPs after screening, we used various databases to carry out functional enrichment of related DEGs to explore their possible influence on a specific aspect of the disease. 
limma
Significances of viable synergistic autophagy-associated cathepsin B and cathepsin D (CTSB/CTSD) as potential biomarkers for sudden cardiac death.BACKGROUND
 The Cathepsins family, including cathepsin B and cathepsin D, potentially affects the entire processes involved in atherosclerosis.  Although coronary heart disease (CHD) has been widely studied as the basis of Sudden Cardiac Death (SCD), the relationship between CHD and CTSB/D remains unclear.


 We screened for differentially expressed proteins (DEPs) associated with autophagy by limma package in R. For the genes corresponding to the DEPs after screening, we used various databases to carry out functional enrichment of related DEGs to explore their possible influence on a specific aspect of the disease.  Functional enrichment analysis of DEGs was performed by DAVID, Metascape and GSEA.  STRING and Cytoscape were obtained the hub genes, the analysis of interaction networks through the GENMANIA and Networkanalyst.  Western Blot was used to validate the protein expression level of target genes.  TF and miRNA prediction were performed using Networkanalyst and visualized using Cytoscape.


 RESULTS
 The expression levels of members of the cathepsin family were up regulated in CHD tissues compared with the control.  GO and KEGG revealed that cathepsin was markedly enriched in endopeptidase activities, immune responses, lysosome pathways, et al.  The correlation analysis showed that in patients with CHD, the CTSB/CTSD expression were negatively correlated with ATG4D and BNIP3, but positively with BCL2L1, CAPNS1, and TP53.  In the TF-mRNA-miRNA network, has-miR-24-3p and has-miR-128-3p had higher degrees, CTSB/CTSD could be targeted by them.


 Our findings elucidated the expression and regulatory role of cathepsins in coronary heart disease induced SCD and might further explore the potential mechanisms of autophagy in CHD.
R
Functional enrichment analysis of DEGs was performed by DAVID, Metascape and GSEA. 
DAVID
Functional enrichment analysis of DEGs was performed by DAVID, Metascape and GSEA. 
Metascape
Functional enrichment analysis of DEGs was performed by DAVID, Metascape and GSEA. 
GSEA
STRING and Cytoscape were obtained the hub genes, the analysis of interaction networks through the GENMANIA and Networkanalyst. 
STRING
STRING and Cytoscape were obtained the hub genes, the analysis of interaction networks through the GENMANIA and Networkanalyst.  TF and miRNA prediction were performed using Networkanalyst and visualized using Cytoscape.



Cytoscape
STRING and Cytoscape were obtained the hub genes, the analysis of interaction networks through the GENMANIA and Networkanalyst. 
GENMANIA
STRING and Cytoscape were obtained the hub genes, the analysis of interaction networks through the GENMANIA and Networkanalyst.  TF and miRNA prediction were performed using Networkanalyst and visualized using Cytoscape.



Networkanalyst
Western Blot was used to validate the protein expression level of target genes. 
Western Blot