Fig. 1

Identification of NAFLD progression-specific pathways and genes. (a) The similarities among all the biological processes (BPs) were measured and visualized, and similar terms were clustered into a common branch. (b) The top five altered GOBPs were displayed in a Circos diagram. (c) WGCNA was performed with the transcriptome profiling data of 98 NAFLD samples and a total of 36 gene modules were identified. The brown module which exhibited the highest correlation with sample category (|r| = 0.61, p = 6e-11) and was considered as “WGCNA-identified gene module of NAFLD progression”. (d) A volcano plot showed a total of 378 DEGs between NAFL and NASH samples with a filtering threshold of q value less than 0.01 and fold change (FC) > 2 or < 0.5. (e) 182 overlapping genes in the intersection of “WGCNA-identified gene module of NAFLD progression” and “DEGs between NAFL and NASH” are considered as “NAFLD progression-specific genes”. (f) A PPI network was generated to depict the functional and physical linkages among these DEGs, and the hub (the red circle) in the network is mainly composed of collagen family members. (g) CMap algorithm showed top 10 compounds with the highest predictive scores and corresponding 7 mode-of-actions (MoAs) in a dot diagram. The 7 MoAs were annotated with “Angiotensin receptor antagonist”, “Aromatic hydrocarbon derivative”, “Aurora kinase inhibitor”, “EGFR inhibitor”, “HDAC inhibitor”, “NFκB pathway inhibitor”, and “Sphingosine kinase inhibitor”