17 Comparison Report: PA/PAAD
- Cancer Category: carcinomas
- Chip hu35ksuba: 221 filtered probes
- Chip hu6800: 520 filtered probes
Overall Complexity & Entropy Assessment
| Measure | All Filtered Probes | GO MF Terms | KEGG Pathways | HALLMARK Genes |
|---|---|---|---|---|
| Complexity | strong loss (uncertain) | () | strong loss (uncertain) | strong loss (uncertain) |
| Shannon Entropy | no clear change (uncertain) | () | no clear change (well supported) | no clear change (well supported) |
| Spectral Entropy | no clear change (uncertain) | () | strongly chaotic (well supported) | mildly chaotic (well supported) |
Notes - Gain = increased complexity from normal to tumor
- Loss = complexity reduction from normal to tumor
- Chaotic = increased entropy from normal to tumor
- Anti-Chaotic = entropy reduction from normal to tumor
- All p-values unadjusted unless noted
Gain Complexity Clusters
| Cluster | # Terms | p-value | Representative Terms |
|---|---|---|---|
| 15 | 1 | 0.024 | positive regulation of T cell mediated cytotoxicity |
| 8 | 2 | 0.354 | positive regulation of gene expression; positive regulation of gene expression |
| 3 | 6 | 0.608 | regulation of transcription by RNA polymerase II; positive regulation of transcription, DNA-templated; positive regulation of transcription by RNA polymerase II |
| 12 | 2 | 0.746 | cellular response to interferon-gamma; cellular response to interferon-gamma |
| * Combined p-values are computed using Fisher’s method (sumlog) across the GO terms in each cluster. |
Loss Complexity Clusters
| Cluster | # Terms | p-value | Representative Terms |
|---|---|---|---|
| 19 | 1 | 0.000 | proteolysis |
| 48 | 1 | 0.000 | positive regulation of stress fiber assembly |
| 7 | 2 | 0.199 | positive regulation of cell population proliferation; positive regulation of cell population proliferation |
| 23 | 2 | 0.277 | actin filament organization; actin cytoskeleton organization |
| 20 | 2 | 0.618 | apoptotic process; neuron apoptotic process |
| 5 | 3 | 0.654 | signal transduction; signal transduction; integrin-mediated signaling pathway |
| 10 | 4 | 0.802 | regulation of apoptotic process; negative regulation of apoptotic process; regulation of apoptotic process |
| 31 | 2 | 0.825 | extracellular matrix organization; collagen fibril organization |
| * Combined p-values are computed using Fisher’s method (sumlog) across the GO terms in each cluster. |
Mixed Complexity Clusters
| Cluster | # Terms | p-value | Representative Terms |
|---|---|---|---|
| 9 | 2 | 0.008 | cell differentiation; osteoblast differentiation |
| * Combined p-values are computed using Fisher’s method (sumlog) across the GO terms in each cluster. |
⚠️ Table not available.
Significant GO Molecular Function Terms (Complexity)
Gained Complexity
| GeneSet | p-value |
|---|---|
| angiogenesis | 0.038 |
| positive regulation of T cell mediated cytotoxicity | 0.024 |
| regulation of cell cycle | 0.029 |
Lost Complexity
| GeneSet | p-value |
|---|---|
| osteoblast differentiation | 0.002 |
| positive regulation of stress fiber assembly | 0.000 |
| proteolysis | 0.000 |
| serine-type endopeptidase activity | 0.033 |
Significant GO Molecular Function Terms (Spectral Entropy)
Strongly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| adaptive immune response | 0.002 |
| signaling receptor binding | 0.003 |
Mildly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| immune response | 0.008 |
| innate immune response | 0.014 |
| positive regulation of T cell mediated cytotoxicity | 0.008 |
Neutral
| GeneSet | p-value |
|---|---|
| RNA binding | 0.031 |
| actin binding | 0.002 |
| cellular response to transforming growth factor beta stimulus | 0.002 |
| defense response to Gram-negative bacterium | 0.031 |
| protein-containing complex binding | 0.021 |
| response to hydrogen peroxide | 0.001 |
| substantia nigra development | 0.044 |
Mildly Chaotic
| GeneSet | p-value |
|---|---|
| ATP binding | 0.038 |
| RNA polymerase II cis-regulatory region sequence-specific DNA binding | 0.010 |
| actin filament binding | 0.029 |
| chromatin remodeling | 0.035 |
| complement activation, classical pathway | 0.031 |
| epithelial cell differentiation | 0.004 |
| extracellular matrix organization | 0.003 |
| identical protein binding | 0.008 |
| integrin binding | 0.004 |
| maintenance of blood-brain barrier | 0.036 |
| platelet aggregation | 0.031 |
| positive regulation of apoptotic process | 0.000 |
| positive regulation of cell migration | 0.006 |
| positive regulation of cell population proliferation | 0.007 |
| regulation of cell migration | 0.021 |
| regulation of transcription by RNA polymerase II | 0.007 |
| regulation of transcription by RNA polymerase II | 0.014 |
| response to xenobiotic stimulus | 0.004 |
| serine-type endopeptidase inhibitor activity | 0.018 |
| signal transduction | 0.021 |
Strongly Chaotic
| GeneSet | p-value |
|---|---|
| antimicrobial humoral immune response mediated by antimicrobial peptide | 0.004 |
| heparin binding | 0.000 |
| positive regulation of I-kappaB kinase/NF-kappaB signaling | 0.003 |
| protease binding | 0.019 |
| protein homodimerization activity | 0.016 |
| proteolysis | 0.029 |
Significant KEGG Pathways (Complexity)
Gained Complexity
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Pathways in cancer | 0.947 | ✅ |
| Systemic lupus erythematosus | 0.032 |
Lost Complexity
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Complement and coagulation cascades | 0.032 | |
| ECM-receptor interaction | 0.012 |
Significant KEGG Pathways (Spectral Entropy)
Mildly Anti-Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Cell adhesion molecule (CAM) interaction | 0.006 |
Neutral
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Phagosome | 0.002 |
Mildly Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Amoebiasis | 0.048 | |
| Arrhythmogenic right ventricular cardiomyopathy | 0.042 | |
| Focal adhesion | 0.026 | |
| Leukocyte transendothelial migration | 0.012 | |
| Regulation of actin cytoskeleton | 0.020 | |
| Tight junction | 0.049 |
Strongly Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Pathways in cancer | 1.000 | ✅ |
Significant HALLMARK Genes (Complexity)
No significant MSigDB gene sets found.
Significant HALLMARK Genes (Spectral Entropy)
Neutral
| GeneSet | p-value |
|---|---|
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 0.041 |
Mildly Chaotic
| GeneSet | p-value |
|---|---|
| HALLMARK_HYPOXIA | 0.042 |
| HALLMARK_MYC_TARGETS_V1 | 0.033 |
Strongly Chaotic
| GeneSet | p-value |
|---|---|
| HALLMARK_COMPLEMENT | 0.018 |