Table 3. Pathway analysis.
The 20 most affected canonical pathways in each NGS dataset with the corresponding values and ranks. Rank indicates the place of the pathway within the list of pathways sorted by largest to smallest –log(adjusted p-value). 12 of 20 pathways are shared between both datasets. TU: tumour, NO: normal, FC: fold change, ND: not detected, did not pass the expression filter.
| FFPE | -log(adj. p-value) | rank | ||
| FFPE | RNAlater® | FFPE | RNAlater® | |
| Antigen Presentation Pathway | 13,90 | 9,13 | 1 | 3 |
| Hepatic Fibrosis / Hepatic Stellate Cell Activation | 13,90 | 14,60 | 2 | 2 |
| LXR/RXR Activation | 7,53 | 6,67 | 3 | 4 |
| Leukocyte Extravasation Signaling | 7,13 | 4,55 | 4 | 9 |
| Coagulation System | 6,78 | 6,59 | 5 | 5 |
| Communication between Innate and Adaptive Immune Cells | 6,60 | 3,58 | 6 | 17 |
| Caveolar-mediated Endocytosis Signaling | 6,54 | 3,69 | 7 | 12 |
| Atherosclerosis Signaling | 6,50 | 6,04 | 8 | 6 |
| Dendritic Cell Maturation | 6,50 | 4,18 | 9 | 10 |
| Crosstalk between Dendritic Cells and Natural Killer Cells | 6,31 | 3,62 | 10 | 14 |
| Graft-versus-Host Disease Signaling | 5,80 | 3,02 | 11 | 35 |
| Complement System | 5,78 | 4,55 | 12 | 8 |
| Autoimmune Thyroid Disease Signaling | 5,78 | 3,49 | 13 | 23 |
| Virus Entry via Endocytic Pathways | 5,78 | 2,92 | 14 | 38 |
| OX40 Signaling Pathway | 5,78 | 3,34 | 15 | 28 |
| Intrinsic Prothrombin Activation Pathway | 5,44 | 4,15 | 16 | 11 |
| Allograft Rejection Signaling | 5,44 | 3,49 | 17 | 25 |
| Fcγ Receptor-mediated Phagocytosis in Macrophages and Monocytes | 4,85 | 3,52 | 18 | 22 |
| Granulocyte Adhesion and Diapedesis | 4,36 | 2,74 | 19 | 47 |
| iCOS-iCOSL Signaling in T Helper Cells | 4,35 | 2,86 | 20 | 41 |
| RNAlater® | -log(adj. p-value) | rank | ||
| RNAlater® | FFPE | RNAlater® | FFPE | |
| EIF2 Signaling | 14,60 | ND | 1 | ND |
| Hepatic Fibrosis / Hepatic Stellate Cell Activation | 14,60 | 13,90 | 2 | 2 |
| Antigen Presentation Pathway | 9,13 | 13,90 | 3 | 1 |
| LXR/RXR Activation | 6,67 | 7,53 | 4 | 3 |
| Coagulation System | 6,59 | 6,78 | 5 | 5 |
| Atherosclerosis Signaling | 6,04 | 6,50 | 6 | 8 |
| LPS/IL-1 Mediated Inhibition of RXR Function | 5,23 | 3,87 | 7 | 27 |
| Complement System | 4,55 | 5,78 | 8 | 12 |
| Leukocyte Extravasation Signaling | 4,55 | 7,13 | 9 | 4 |
| Dendritic Cell Maturation | 4,18 | 6,50 | 10 | 9 |
| Intrinsic Prothrombin Activation Pathway | 4,15 | 5,44 | 11 | 16 |
| Caveolar-mediated Endocytosis Signaling | 3,69 | 6,54 | 12 | 7 |
| Ethanol Degradation II | 3,62 | 1,49 | 13 | 77 |
| Crosstalk between Dendritic Cells and Natural Killer Cells | 3,62 | 6,31 | 14 | 10 |
| Histamine Degradation | 3,58 | 0,41 | 15 | 267 |
| B Cell Development | 3,58 | 3,15 | 16 | 32 |
| Communication between Innate and Adaptive I Immune Cells | 3,58 | 6,60 | 17 | 6 |
| eNOS Signaling | 3,58 | 2,78 | 18 | 41 |
| Valine Degradation I | 3,57 | 1,48 | 19 | 78 |
| mTOR Signaling | 3,57 | ND | 20 | ND |