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Table 10 Summary of IPA analyses of RNAs obtained from δ-tocotrienol treatment of hepatitis C patients

From: δ-Tocotrienol feeding modulates gene expression of EIF2, mTOR, protein ubiquitination through multiple-signaling pathways in chronic hepatitis C patients

# Subjects P-Value ovrlap Overlap # Subjects P-Value ovrlap # Molecules
I Top Canonical Pathways    VII Cardiotoxicity   
1 EIF2 Signaling 1.28E-37 30.3 % 67/221 31 Cardiac Infarction 3.62E-01 - 5.40E-04 23
2 Regulation of eIF4 and p70S6K Signaling 5.38 E-140 21.0 % 33/157 32 Caediac Necrosis/Cell Death 1.65E-01 - 2.56E-03 23
3 mTOR Signaling 1.28 E-13 18.4 % 37/102 33 Cardiac Dycfunction 4.31E-01 - 2.63E-03 11
4 B Cell Receptor Signaling 8.35 E-08 14.2 % 27/190 34 Cardiac Fibrosis 1.77E-01 - 5.68E-03 14
5 Signaling 1.72E-06 16.2 % 18/111 35 Cardiac Transformation 1.10E-02 - 1.10E-02 2
II Top Upstream Regulators   Predicted Activation VIII Hepatotoxicity   
6 ST 1926 5.62E-20 Activated 36 Liver Proliferation 2.15E-01 - 5.85E-05 26
7 Sirolimus 2.32E-18 Activated 37 Liver Necrosis/Cell Death 6.13E-01 - 6.59E-05 29
8 CD 437 1.45E-17 Activated 38 Liver Damage 4.69E-01 - 1.81E-04 35
9 RICTOR 1.64E-17 Activated 39 Liver Inflamma/Hepatitistion 4.52E-01 - 5.02E-04 36
10 MYCN 3.22E-15 Inhibited 40 Liver Cirrhosis 4.19E-02 - 1.65E-03 21
III Diseases and Disorder   # Molecules IX Nephrotoxicity   
11 Infectious Diseases 1.14E-04 - 1.29E-24 244 41 Renal Necrosis/Cell Death 3.32E-01 - 7.15E-05 46
12 Immunological Disease 7.41E-05 - 2.37E-23 372 42 Renal Inflammation 3.74E-01 - 1.69E-03 33
13 Cancer 1.25E-04 - 4.75E-22 839 43 Renal Nephritis 3.70E-01 - 1.69E-03 33
14 Organismal Injury and Abnormalities 1.36E-04 - 4.75E-21 865 44 Renal Damage 5.15E01 - 3.12E-03 21
15 Tumor Morphology 1.19E-04 - 4.75E-21 82 45 Glomerular Injury 1.00E-00 - 1.47E-02 22
IV Molecular and Cellular Functions   # Molecules X Top Regulator Effect Networks Disease & Functions Consistency Score
16 Cellular Development 1.24E-04 - 1.29E-24 222 46 Ap1,CAMP,F2RL1,IL17A,IL1RN,KITLG,mir10,NRG1,SELP (+2 >) Activationof antigen presenting cells (+11 >) 40.848
17 Cellular Growth and Proliferation 1.24E-04 - 1.29E-24 206 47 AP1,CAMP,EIF2AK2,F2RL1,IL17A,IL1RN, KITLG (+2 >) Activationof phagocytes (+9 >) 36.338
18 Cell Death and Survival 1.36E -04 - 3.94E-21 371 48 26s Proteasome,ANGPT2,AP1,BCL2,CAMP,CEBPA,F2RL (+6 >) Activationof antigen presenting cells (+10 >) 32.199
19 Cell-To-Cell Signalingand Interaction 1.34EE-18-04 - 7.04 183 49 26s Proteasome,CAMP,CSF1,IL17A,JUN,LDL (+5 >)F2RL (+6 >) Activationof antigen presenting cells (+7 >) 30.414
20 Cellular Function and Maintenance 1.02E-04 - 2.10E-16 232 50 AP1,CAMP,CCL5,EIF2AK2,F2RL1,FGF10,IL17A,IL1RN (+5 >) Accumulation of leukocytes (+19 >) 30.375
V Physiological System Development and Function   # Molecules XI Top Networks (Associated Network Functions)   Score
21 Hematological System Development and Function 1.34E-04 -1.29E-24 255 51 Developmentall Disorder, Hereditary Disorder, Metabolic Diseases 46
22 Lymphoid Tissue Structure and Development 1.33E-04 -1.29E-24 194 52 Cancer, Cell Death and Survival, Organismal Injury and Abnormalities 44
23 Tissue Morphology 1.19E-04 - 2.45E-19 184 53 Post-Translational Midification, Cell Cycle, Cellular Development 44
24 Immune Cell Trafficking 1.34E-04 - 7.04E-18 160 54 Cancer, Hematological Disease, Immunological Disease   41
25 Hematopoiesis 1.02E004 - 6.87E-14 130 55 Protein Synthesis, RNA Post-Transcriptional Modification, Gene Expression 39
VI Top Tox Functions (Clinical Chemistry and Hematology)   # Molecules XII Top Toxicology Lists p-value Overlap
26 Increased Levels of Albumin 2.38E-01 - 1.24E-02 4 56 Renal Necrosis/Cell Death 1.58E-05 8.60 % 46/538
27 Increased Levels of Alkaline Phosphatase 2.12E-01 - 4,42E-02 6 57 Liver Prolification 1.80E-05 11.0 % 26/236
28 Decreased Levels of Hematocrit 5.71E-02 - 5.71E-02 2 58 Liver Necrosis/ Cell Death 8.35E-05 9.6 % 29/303
29 Increased Levels of Hematocrit 6.20E-02 - 6,20E-02 8 59 Mechanism of Gene regulation by Peroxisome 2.74E-04 13.7 % 13/95
30 Increased Levels of Potassium 5.36E-01 - 8.64E-02 2 60 Increases Liver Damage 7.40E-04 11.4 % 15/132
A Gene Expression Fold Change (Up-regulated) Expression Value   B Gene Expression Fold Change (Down-regulated) Expression Value  
1 SNORD15A 581.151   1 HMGN1P3 -381.06  
2 SNORA32 390.353   2 SNHG25 -350.0555  
3 SNORA56 185.194   3 SNORA67 -148.69  
4 SNORA9 124.698   4 RPL17-C18orf32 -67.253  
5 SNORS3B 102.91   5 ISY1-RAB43 -51.147  
6 SNORA3A 93.09   6 ARHGEF18 -41.381  
7 HIST1H2AD 20.784   7 KLRC4-KLRK1/KLK1 -20.578  
8 SNORD3D 17.157   8 HIST1H3J -19.795  
9 LINC00305 4.853   9 MTHFS -18.71  
10 HHIPL2 4.844   10 SNORA16A -18.285