11 Comparison Report: BLAD/TCC
- Cancer Category: carcinomas
- Chip hu35ksuba: 3259 filtered probes
- Chip hu6800: 399 filtered probes
Overall Complexity & Entropy Assessment
| Measure | All Filtered Probes | GO MF Terms | KEGG Pathways | HALLMARK Genes |
|---|---|---|---|---|
| Complexity | strong loss (uncertain) | () | strong gain (moderately supported) | strong loss (moderately supported) |
| Shannon Entropy | no clear change (uncertain) | () | no clear change (moderately supported) | no clear change (well supported) |
| Spectral Entropy | no clear change (uncertain) | () | strongly anti-chaotic (moderately supported) | mildly anti-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 |
|---|---|---|---|
| 29 | 2 | 0.008 | endoplasmic reticulum to Golgi vesicle-mediated transport; endosomal transport |
| 50 | 2 | 0.023 | regulation of cell shape; regulation of cell shape |
| 98 | 1 | 0.030 | defense response to virus |
| 42 | 4 | 0.092 | Notch signaling pathway; integrin-mediated signaling pathway; SMAD protein signal transduction |
| 4 | 3 | 0.181 | microtubule cytoskeleton organization; cytoskeleton organization; cytoskeleton organization |
| 86 | 3 | 0.220 | positive regulation of I-kappaB kinase/NF-kappaB signaling; positive regulation of protein kinase B signaling; positive regulation of protein kinase B signaling |
| 38 | 3 | 0.260 | cell adhesion; cell-cell adhesion; cell adhesion |
| 46 | 3 | 0.277 | brain development; substantia nigra development; substantia nigra development |
| 53 | 2 | 0.339 | response to wounding; wound healing |
| 28 | 2 | 0.364 | intracellular protein transport; protein transport |
| 87 | 3 | 0.424 | positive regulation of MAPK cascade; positive regulation of ERK1 and ERK2 cascade; positive regulation of ERK1 and ERK2 cascade |
| 13 | 3 | 0.561 | tissue homeostasis; maintenance of blood-brain barrier; maintenance of blood-brain barrier |
| 33 | 2 | 0.580 | muscle contraction; muscle contraction |
| 8 | 2 | 0.584 | angiogenesis; angiogenesis |
| 41 | 3 | 0.787 | transforming growth factor beta receptor signaling pathway; BMP signaling pathway; transforming growth factor beta receptor signaling pathway |
| 32 | 3 | 0.794 | apoptotic process; neuron apoptotic process; neuron apoptotic process |
| 54 | 2 | 0.896 | response to mechanical stimulus; response to mechanical stimulus |
| 10 | 3 | 0.955 | osteoblast differentiation; cell differentiation; cell differentiation |
| * 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 |
|---|---|---|---|
| 48 | 3 | 0.006 | positive regulation of cell population proliferation; regulation of cell population proliferation; positive regulation of cell population proliferation |
| 111 | 2 | 0.029 | regulation of synaptic vesicle endocytosis; regulation of synaptic vesicle endocytosis |
| 114 | 1 | 0.032 | positive regulation of double-strand break repair via homologous recombination |
| 7 | 1 | 0.041 | cell morphogenesis |
| 116 | 1 | 0.046 | regulation of double-strand break repair |
| 65 | 3 | 0.082 | cell migration; cell motility; cell motility |
| 99 | 2 | 0.113 | regulation of cell cycle; regulation of cell cycle |
| 45 | 3 | 0.127 | axonogenesis; neuron projection morphogenesis; axonogenesis |
| 88 | 2 | 0.141 | innate immune response; innate immune response |
| 3 | 3 | 0.180 | negative regulation of transcription by RNA polymerase II; negative regulation of transcription, DNA-templated; negative regulation of transcription by RNA polymerase II |
| 49 | 2 | 0.291 | negative regulation of cell population proliferation; negative regulation of cell population proliferation |
| 20 | 4 | 0.389 | regulation of transcription, DNA-templated; regulation of transcription by RNA polymerase II; negative regulation of NF-kappaB transcription factor activity |
| 15 | 5 | 0.454 | cytoplasmic translation; translation; translational initiation |
| 52 | 2 | 0.474 | response to xenobiotic stimulus; response to xenobiotic stimulus |
| 94 | 4 | 0.609 | positive regulation of transcription, DNA-templated; positive regulation of transcription by RNA polymerase II; positive regulation of transcription, DNA-templated |
| 84 | 3 | 0.641 | negative regulation of apoptotic process; negative regulation of neuron apoptotic process; negative regulation of apoptotic process |
| 55 | 2 | 0.802 | response to bacterium; defense response to bacterium |
| 21 | 3 | 0.942 | RNA processing; mRNA processing; RNA splicing |
| * 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 |
|---|---|---|---|
| 23 | 2 | 0.032 | protein phosphorylation; protein autophosphorylation |
| * 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 |
|---|---|
| ATPase | 0.038 |
| cytoskeleton organization | 0.047 |
| defense response to virus | 0.030 |
| endoplasmic reticulum to Golgi vesicle-mediated transport | 0.002 |
| neuron apoptotic process | 0.000 |
| regulation of cell shape | 0.010 |
| small GTPase binding | 0.025 |
Lost Complexity
| GeneSet | p-value |
|---|---|
| cell morphogenesis | 0.041 |
| cell motility | 0.025 |
| in utero embryonic development | 0.000 |
| integrin-mediated signaling pathway | 0.031 |
| metal ion binding | 0.019 |
| negative regulation of transcription by RNA polymerase II | 0.023 |
| nitric-oxide synthase binding | 0.042 |
| positive regulation of cell population proliferation | 0.028 |
| positive regulation of double-strand break repair via homologous recombination | 0.032 |
| protein autophosphorylation | 0.022 |
| regulation of cell population proliferation | 0.012 |
| regulation of double-strand break repair | 0.046 |
| regulation of synaptic vesicle endocytosis | 0.046 |
| regulation of transcription, DNA-templated | 0.030 |
Significant GO Molecular Function Terms (Spectral Entropy)
Strongly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| cell differentiation | 0.048 |
| negative regulation of canonical Wnt signaling pathway | 0.032 |
| response to hypoxia | 0.031 |
Mildly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| extracellular matrix structural constituent | 0.004 |
| identical protein binding | 0.015 |
| integrin binding | 0.050 |
| muscle contraction | 0.020 |
| negative regulation of protein kinase activity | 0.018 |
| positive regulation of gene expression | 0.028 |
| protein binding | 0.005 |
| protein homodimerization activity | 0.031 |
| protein serine kinase activity | 0.020 |
Neutral
| GeneSet | p-value |
|---|---|
| GTPase activator activity | 0.041 |
| GTPase activity | 0.039 |
| RNA binding | 0.032 |
| cell motility | 0.018 |
| positive regulation of cell population proliferation | 0.046 |
| regulation of synaptic vesicle endocytosis | 0.025 |
| response to wounding | 0.048 |
| structural constituent of ribosome | 0.027 |
Mildly Chaotic
| GeneSet | p-value |
|---|---|
| ATPase | 0.014 |
| Tat protein binding | 0.010 |
| apical protein localization | 0.027 |
| brain development | 0.037 |
| negative regulation of cell differentiation | 0.024 |
| positive regulation of T cell differentiation | 0.024 |
| positive regulation of myoblast differentiation | 0.039 |
| regulation of protein localization to plasma membrane | 0.008 |
| response to bacterium | 0.043 |
| structural molecule activity | 0.010 |
Strongly Chaotic
| GeneSet | p-value |
|---|---|
| intracellular protein transport | 0.003 |
| protein-containing complex binding | 0.016 |
Significant KEGG Pathways (Complexity)
Gained Complexity
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Pathways in cancer | 0.041 | ✅ |
| Protein processing in endoplasmic reticulum | 0.001 | |
| Tight junction | 0.013 |
Significant KEGG Pathways (Spectral Entropy)
Strongly Anti-Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Tight junction | 0.034 |
Mildly Anti-Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Focal adhesion | 0.026 | |
| Pathways in cancer | 0.082 | ✅ |
Mildly Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Nucleocytoplasmic transport | 0.038 |
Strongly Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Leukocyte transendothelial migration | 0.047 |
Significant HALLMARK Genes (Complexity)
Lost Complexity
| GeneSet | p-value |
|---|---|
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.028 |
| HALLMARK_UV_RESPONSE_DN | 0.042 |
Significant HALLMARK Genes (Spectral Entropy)
Mildly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| HALLMARK_COMPLEMENT | 0.022 |
Neutral
| GeneSet | p-value |
|---|---|
| HALLMARK_UV_RESPONSE_DN | 0.025 |