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. 2010 Mar 26;16(7-8):287–297. doi: 10.2119/molmed.2009.00165

Table 1.

Summary of the more important findings for each analysis.a

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 (P 8.57E-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)		 Not applicable
a

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