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Table 1 Summary of the more important findings for each analysis.a

From: Molecular Mechanisms Involved in the Interaction Effects of Alcohol and Hepatitis C Virus in Liver Cirrhosis

 

Alcohol cirrhotic tissues versus normal livers

HCV cirrhotic tissues versus normal livers

HCV versus alcohol cirrhotic tissues

Significant interaction analysis

Number of differentially expressed probe sets/genes

1406/1272

2222/1841

2172/1896

1230/1051

Associated Network Functions (five top-scored networks)

1. Protein degradation, protein synthesis, immunological disease (score 37);

2. Gene expression, cancer, infectious disease (score 37);

3. Cell morphology, tissue morphology, RNA damage and repair (score 35);

4. Cell cycle, cancer, gastrointestinal disease (score 35);

5. Cell cycle, cellular development, skeletal and muscular system development and function (score 35)

1. Molecular transport, connective tissue disorders, dermatological diseases and conditions (score 43);

2. Cell death, molecular transport, cellular assembly and organization (score 40);

3. Lymphoid tissue structure and development, organ development, cellular development (score 37);

4. Gene expression, lipid metabolism, molecular transport (score 37);

5. Cancer, immunological disease, organismal development (score 35)

1. Lipid metabolism, small molecule biochemistry, molecular transport (score 42);

2. Protein synthesis, infection mechanism, nervous system development and function (score 39);

3. Gene expression, connective tissue development and function, skeletal and muscular system development and function (score 37);

4. Gene expression, lipid metabolism, small molecule biochemistry (score 37);

5. Molecular transport, RNA posttranscriptional modification, RNA trafficking (score 34)

1. Genetic disorder, hematological disease, cell cycle (score 45);

2. Cancer, cell death, reproductive system disease (score 40);

3. Lipid metabolism, small-molecule biochemistry, cellular movement (score 38);

4. Hematological disease, genetic disorder, cellular assembly and organization (score 38);

5. Protein trafficking, developmental disorder, genetic disorder (score 38)

Top molecular and cellular functions

Cellular growth and proliferation (P 1.47E-04 to 4.24E-02), 314 genes

Gene expression (P 1.92E-04 to 3.81E-02), 236 genes

Cell Cycle (P 4.81E-04 to 4.42E-02) 148 genes

Amino acid metabolism (P 7.68E-04 to 4.51E- 02), 54 genes

Posttranslational modification (P 7.68E-04 to 4.38E-02), 135 genes

Cellular growth and proliferation (P 1.12E-13 to 4.03E-03), 402 genes

Cell death (P 2.80E-13 to 3.90E-03), 361 genes

Cellular movement (P 2.88E-12 to 3.83E-03), 211 genes

Cellular development (P 1.76E- 09 to 3.76E-03), 260 genes

Cell-to-cell signaling and interaction (P 6.38E-08 to 4.26E-03), 248 genes;

Gene expression (P 1.49E-09 to 1.21E-02), 285 genes

RNA posttranscriptional modification; (P 2.50E-09 to 7.19E-05), 51 genes

Cell death (P 1.35E-07 to 1.21E-02), 326 genes

Cellular growth and proliferation (P 2.20E-07 to 1.21E-02), 354 genes

Protein synthesis (P 2.47E-06 to 5.74E- 03), 107 genes

Cell death (P 1.00E-08 to 2.19E-02), 228 genes

Cellular growth and proliferation (P8.57E-08 to 2.12E-02), 267 genes

Cellular compromise (P 2.88E-05 to 1.17E-02), 14 genes

Cell morphology (P 3.36E-05 to 2.21E-02), 144 genes

Cell-to-cell signaling and interaction (P 6.79E-05 to 1.63E-02) 96 genes

Top canonical pathways

JAK/Stat signaling (P = 5.39E-04), Protein ubiquitination pathway (P = 8.22E-04), VEGF signaling (P = 1.06E-03)

Hepatic fibrosis/hepatic stellate cell activation (P = 9.17E-06), Phospholipase C signaling (P = 1.62E- 05), G-protein-coupled receptor signaling (P = 3.46E-05), Thrombin signaling (P = 4.21E-05)

Death-receptor signaling (P= 1.12E-04), ILK signaling (P = 1.82E-04), B-cell-receptor signaling (P = 6.3E-04)

Antigen-presentation pathway (P = 7.92E-07), IL-4 signaling (P = 6.92E-03), Riboflavin metabolism (P = 1.27E-02), Hepatic fibrosis/hepatic stellate cell activation (P = 1.32E-02) coagulation system (P = 2.19E-02)

Top overexpressed genes (fold changes)

NTN3 (19.62) IGKC (11.95) IGL@ (10.56) HLA-C (7.08) IGHM (6.8) HBB (includes EG:3043) (6.65) ZCWPW2 (includes EG:152098) (5.73) MAFF (5.51) IL8 (5.4) HBA1 (5.26)

IFI27 (21.72) NTN3 (19.62) IGKC (16.04) CXCL10 (10.89) IGL@ (10.56) HLA-DQB1 (9.98) IFIT1 (9.07) AKR1B10 (8.09) HBB(includes EG:3043) (8.01) IGHM(7.68)

IFI27 (11.7) ISG15 (5.73) CXCL10 (5.68) IFIT1 (5.13) MX1 (4.09) HSP90B1 (4.06) ID1 (3.73) ISG20 (3.66) IFI44 (3.33) MCL1 (3.27)

Not applicable

Top underexpressed genes (fold changes)

S100A8 (−5.57) FCN2 (−3.58) RFC5 (−3.54) SAA2 (−3.47) TFPI (−3.30) ST6GAL1 (−3.1) KCNN2 (−3.1) ABCA1 (−2.99) TGM2 (−2.97) LMAN1 (−2.95)

LPA (−4.5) ATF5 (−4.49) STEAP1 (−3.8) PZP (−3.63) SAA2 (−3.47) MT1M (−3.45) TFPI (−3.3) DHODH (−3.3) SLCO4C1 (−3.2) KCNN2 (−3.1)

BBOX1 (−4.75) ATP8B1 (−4.0) SLC35E1 (−2.55) PRG2 (includes EG:79948) (−2.46) RBM25 (includes EG:58517) (−2.41) DBP (−2.39) ZC3H7Ba (−2.37) POLR1B (−2.26) UBB (−2.21) FGFR1 (−2.20)

Not applicable

  1. aAnalysis performed by using Ingenuity Pathways Analysis tools 7.0 (http://www.ingenuity.com).