Raw data VS. Residual value B 1898 766 44 C 2169 495 80 Supporting Fig. 1. Neither age nor gender were major drivers of expression differences between the control and NAFLD groups. (A) The cumulative curve of coefficient of variation of gene expression. (B) Overlap between differentially expressed genes using either the residual values from age or the raw data. (C) Overlap between differentially expressed genes using either the residual values from gender or the raw data.

Scaled expression values -3 1 3 Age (years) 0 35 70 Supporting Fig. 2. Gene expression in NAFLD. Heat map of top 200 genes variant expressed between control, NAFL and NAFLD samples. Scaled expression values are color-coded according to the legend on the left. The top bar shows the disease status: red, NASH; green, NAFL; black, control. The bottom bars show additional variables for each sample: age and gender (black, female; grey, male; green, missing value). The scale for age is shown on the left.

Color key 0.9 1 Supporting Fig. 3. Hierarchical clustering of microarray samples based on inter-array correlation showing distinct clustering of NASH, NAFL and control samples. The heatmap shown the square inter-array correlation matrix(IAC). IAC coefficients were calculated using Pearson correlation. The scale for IAC was shown on the left. The upper bar show age for each sample (green, female; blue, male; white, missing value). The scale for age is shown on the left side(white, missing value).

Control NASH A Control NASH B -0.2 0.0 0.2 0.4 Eigengene expression -0.2 0.0 0.2 0.4 Eigengene expression Control NASH B Eigengene expression -0.2 0.0 0.2

Control NASH C -0.4 0.2 0.0 0.2 0.4 Eigengene expression Supporting Fig. 4. Expression within NASH modules N1, N8 and N14 is shown in the heat-map and summarized with the module. The visualization of these modules was performed using VisANT to plot the 100 strongest connections within each module. Genes that are positively correlated are connected by red lines, whereas genes that are inversely correlated are connected by blue lines. (A) The module N1 is involved in chromosome organization. (B) The module N8 contains genes participate in protein degradation. (C) The module N14 contains genes involved in immune response.

NAFL NASH A NAFL NASH B -0.4 0.2 0.0 0.2 Eigengene expression -0.4 0.2 0.0 0.2 Eigengene expression NAFL NASH B -0.3 0.0 0.3 Eigengene expression

NAFL NASH C NAFL NASH D Eigengene expression -0.4 0.2 0.0 0.2 -0.4 0.2 0.0 0.2 Eigengene expression NAFL NASH D -0.2 0.0 0.2 0.4 Eigengene expression

NAFL NASH E NAFL NASH F -0.2 0.0 0.2 0.4 Eigengene expression -0.2 0.0 0.2 0.4 Eigengene expression NAFL NASH F Eigengene expression -0.2 0.0 0.2 0.4

NAFL NASH G Eigengene expression -0.2 0.0 0.2 0.4 Supporting Fig. 5. Expression within progression modules P1(A), P2(B), P5(C), P7(D), P9(E), P13(F) and P14(G) is shown in the heat-map and summarized with the module. The visualization of these modules was performed using VisANT to plot the 100 strongest connections within each module. Genes that are positively correlated are connected by red lines, whereas genes that are inversely correlated are connected by blue lines.

Supporting Fig. 6. To test the stability of modules, intramodular connectivity in 1000 module gene sets generated by sampling 13 of the 26 array samples were calculated for each module. Then, correlations between the true module gene connectivity values and those from the 1000 randomly selected sets were calculated.

Module-miRNA relationships -1 -0.5 0.5 1 MIR24-2 MIR122 MIR27B MIR148B MIR30E MIRLET7G MIRLET7D MIR192 MIR101-2 MIR24-1 MIRLET7F1 MIR29C MIR23B MIR105-2 MIR15A -0.52 (0.006) 0.45 (0.02) 0.3 (0.1) 0.27 (0.2) 0.29 0.38 (0.06) 0.43 (0.03) 0.42 0.33 0.16 (0.4) 0.11 (0.6) 0.19 0.26 -0.04 (0.8) 0.52 0.53 0.51 (0.008) 0.46 0.49 (0.01) 0.2 (0.3) 0.32 0.44 0.41 (0.04) 0.35 (0.08) 0.1 -0.058 -0.1 0.062 -0.21 0.067 (0.7) -0.019 (0.9) -0.2 -0.082 -0.18 0.12 0.024 0.21 -0.56 (0.003) 0.73 (2e-05) 0.67 (2e-04) 0.7 (7e-05) 0.59 (0.002) 0.62 (7e-04) 0.36 (0.07) 0.6 (0.001) 0.37 0.47 (0.005) 0.39 (0.05) 0.31 0.17 0.56 0.34 (0.09) 0.078 0.55 -0.087 -0.17 -0.36 -0.072 -0.022 -0.064 0.053 -0.11 -0.43 0.086 -0.55 (0.004) -0.44 -0.49 -0.57 -0.26 -0.24 -0.32 -0.37 -0.16 -0.27 -0.25 0.65 (3e-04) -0.64 (5e-04) -0.48 -0.61 (9e-04) -0.53 -0.82 (3e-07) -0.35 -0.23 -0.3 -0.51 (6e-05) -0.33 -0.19 -0.63 -0.28 -0.061 0.019 -0.071 -0.033 -0.043 0.001 (1) 0.14 (0.5) 0.24 0.22 0.28 0.07 0.23 0.054 0.0075 0.0083 0.049 -0.29 -0.41 0.0033 -0.22 -0.39 -0.079 -0.12 0.048 -0.13 -0.011 -0.31 0.021 0.13 -0.096 0.68 (1e-04) -0.4 -0.38 (4e-04) -0.037 -0.34 (0.007) 0.4 -0.14 -0.085 0.02 P1 P2 P3 P4 P5 P6 P7 P8 P9 P10 P11 P12 P13 P14 Supporting Fig. 7. Module-miRNA associations in progression network. Each row corresponds to a module eigengene, column to a miRNA. Each cell contains the corresponding correlation and P-value (bracket). The table is color-coded by correlation according to the color legend.

A B C D

E F G H

I J K L

M Supporting Fig. 8. The individual gene expression of the candidates between control, NAFL and NASH groups were shown. MT1DP(A), MT1X(B), PDIA6(C), SRPRB(D), TCF4(E), RPL8(F), IGHG1(G), NANS(H), VIM(I), PTGS2(J), PAN3(K), YIF1A(L) and SRRM2(M)

** A 37 21 55 ** 16 21 70 B C ** 12 2 D ** 93 19 7 NAFL NASH GO category/KEGG pathway S1 N5 Sterol biosynthetic process 6.3E-29 3.4E-27 Lipid biosynthetic process 2.8E-20 8.9E-24 Endoplasmic reticulum 3.4E-4 5.8E-6 Microsome 6.2E-4 8.0E-5 ** A 37 21 55 GO category/KEGG pathway S2 N6 Oxidation reduction 9.9E-8 8.6E-15 Microsome 2.1E-13 2.4E-13 Endoplasmic reticulum 1.5E-8 3.8E-8 Drug metabolism 1.4E-20 1.1E-16 ** 16 21 70 B GO category/KEGG pathway S4 N7 Ion homeostasis 2.6E-2 8.0E-2 Cadmium ion binding 3.5E-16 3.3E-19 Copper ion binding 2.8E-13 4.1E-15 Zinc ion binding 4.1E-4 2.8E-4 C ** 12 2 D ** GO category/KEGG pathway S6 N13 M phase 1.5E-56 1.4E-52 Spindle 3.6E-30 1.4E-26 Chromosome 2.2E-23 6.1E-25 P53 signaling pathway 2.1E-2 1.4E-3 93 19 7

GO category/KEGG pathway S9 N11 RNA processing 2.4E-11 7.8E-4 DNA repair 8.8E-5 NS Spliceosome 4.1E-6 Ubiquitin mediated proteolysis 7.7E-3 E * 20 892 61 GO category/KEGG pathway S10 N14 Innate immune response 1.9E-7 9.6E-10 Adaptive immune response 1.9E-5 2.3E-5 MHC class II receptor activity 1.2E-2 NS Cell adhesion molecules (CAMs) 6.5E-3 1.1E-4 F ** 70 42 43 GO category/KEGG pathway S13 N8 Negative regulation of protein ubiquitination 2.8E-19 1.0E-11 Positive regulation of protein ubiquitination 8.2E-18 9.4E-12 Regulation of protein modification process 7.3E-7 4.9E-5 Proteasome 6.7E-21 6.3E-16 G ** 77 424 392 Supporting Fig. 9. Modules from NAFL analysis overlap significantly with modules from NASH analysis, as measured by both gene number and gene ontology categories enrichment P value from DAVID. *P<0.001; **P<10-9. P values were obtained using a hypergeometric distribution.