Data Bioinformatics Analysis

Differential expressed (DE) mRNA and protein in IL vs NL were identified using two-sided Student’s t-test through OmicShare tools (http://www.omicshare.com/tools), based on two criteria of 1.5-fold change (FC) increase or decrease in expression levels and p-value < 0.05. Gene ontology (GO) terms in biological processes (BP), cellular components (CC), and molecular functions (MF) were enriched using DAVID v6.8, taking p-value < 0.05 as a threshold. Pathway analysis was conducted using KOBAS 3.0, and a p-value < 0.05, corrected by Benjamini-Hochberg method, was considered significant (13, 14). Principal component analysis (PCA) was conducted using the PCA function in the R package FactoMineR. PANTHER was used for protein classification (15). Gene set enrichment analysis (GSEA) was performed using the pre-ranked method in GSEA Java implementation (16), Molecular signatures database (MsigDB, http://software.broadinstitute.org/gsea/msigdb) was used for the gene sets (17); for each category, a p-value < 0.05 was considered significant. The protein–protein interaction (PPI) network of DE proteins was constructed by the Cytoscape (version 3.7.2) STRING APP tool (18). Correlation of mRNAs and protein expression levels was generated using the R corrplot function.