19 Comparison Report: Brain/GBM
- Cancer Category: blastomas
- Chip hu35ksuba: 848 filtered probes
- Chip hu6800: 716 filtered probes
Overall Complexity & Entropy Assessment
| Measure | All Filtered Probes | GO MF Terms | KEGG Pathways | HALLMARK Genes |
|---|---|---|---|---|
| Complexity | strong loss (uncertain) | () | strong loss (moderately supported) | strong loss (moderately supported) |
| Shannon Entropy | no clear change (uncertain) | () | no clear change (uncertain) | no clear change (moderately supported) |
| Spectral Entropy | no clear change (uncertain) | () | strongly anti-chaotic (uncertain) | no clear change (uncertain) |
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 |
|---|---|---|---|
| 39 | 2 | 0.000 | positive regulation of cell differentiation; positive regulation of myoblast differentiation |
| 44 | 1 | 0.003 | regulation of G0 to G1 transition |
| 48 | 1 | 0.003 | positive regulation of double-strand break repair |
| 34 | 1 | 0.004 | regulation of mitotic metaphase/anaphase transition |
| 45 | 1 | 0.004 | platelet aggregation |
| 49 | 1 | 0.005 | regulation of nucleotide-excision repair |
| 46 | 1 | 0.006 | positive regulation of stem cell population maintenance |
| 47 | 1 | 0.023 | regulation of G1/S transition of mitotic cell cycle |
| 37 | 1 | 0.024 | positive regulation of T cell differentiation |
| 29 | 1 | 0.047 | axonogenesis |
| 22 | 2 | 0.753 | cytoplasmic translation; translation |
| * 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 |
|---|---|---|---|
| 2 | 1 | 0.014 | mRNA splicing, via spliceosome |
| 4 | 2 | 0.051 | chromatin remodeling; chromatin remodeling |
| 11 | 3 | 0.119 | regulation of gene expression; positive regulation of gene expression; positive regulation of gene expression |
| 23 | 2 | 0.215 | generation of precursor metabolites and energy; cellular respiration |
| 8 | 2 | 0.227 | nervous system development; nervous system development |
| 1 | 4 | 0.247 | negative regulation of transcription by RNA polymerase II; negative regulation of transcription, DNA-templated; negative regulation of transcription by RNA polymerase II |
| 3 | 2 | 0.523 | osteoblast differentiation; osteoblast differentiation |
| 5 | 7 | 0.793 | regulation of transcription, DNA-templated; regulation of transcription by RNA polymerase II; positive regulation of transcription, DNA-templated |
| 7 | 4 | 0.795 | signal transduction; G protein-coupled receptor signaling pathway; intracellular signal transduction |
| 12 | 2 | 0.835 | cell migration; cell migration |
| * 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 |
|---|---|---|---|
| 6 | 2 | 0.017 | inflammatory response; inflammatory response |
| 19 | 2 | 0.019 | proton transmembrane transport; proton transmembrane transport |
| 38 | 2 | 0.019 | negative regulation of cell differentiation; negative regulation of fat cell 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 |
|---|---|
| Tat protein binding | 0.002 |
| axonogenesis | 0.047 |
| collagen binding | 0.006 |
| negative regulation of cell differentiation | 0.005 |
| nucleosomal DNA binding | 0.007 |
| platelet aggregation | 0.004 |
| positive regulation of T cell differentiation | 0.024 |
| positive regulation of cell differentiation | 0.004 |
| positive regulation of double-strand break repair | 0.003 |
| positive regulation of myoblast differentiation | 0.004 |
| positive regulation of stem cell population maintenance | 0.006 |
| regulation of G0 to G1 transition | 0.003 |
| regulation of G1/S transition of mitotic cell cycle | 0.023 |
| regulation of apoptotic process | 0.008 |
| regulation of mitotic metaphase/anaphase transition | 0.004 |
| regulation of nucleotide-excision repair | 0.005 |
| structural constituent of cytoskeleton | 0.022 |
Lost Complexity
| GeneSet | p-value |
|---|---|
| chromatin remodeling | 0.018 |
| enzyme binding | 0.020 |
| inflammatory response | 0.036 |
| mRNA splicing, via spliceosome | 0.014 |
| negative regulation of transcription by RNA polymerase II | 0.011 |
| proton transmembrane transport | 0.009 |
Significant GO Molecular Function Terms (Spectral Entropy)
Strongly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| signal transduction | 0.025 |
Mildly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| positive regulation of gene expression | 0.005 |
| protein kinase binding | 0.049 |
| proton transmembrane transport | 0.027 |
| zinc ion binding | 0.000 |
Neutral
| GeneSet | p-value |
|---|---|
| Tat protein binding | 0.016 |
| inflammatory response | 0.018 |
| negative regulation of cell differentiation | 0.013 |
| nucleosomal DNA binding | 0.015 |
| positive regulation of double-strand break repair | 0.018 |
| positive regulation of myoblast differentiation | 0.011 |
| positive regulation of stem cell population maintenance | 0.016 |
| protein homodimerization activity | 0.021 |
| regulation of G0 to G1 transition | 0.027 |
| regulation of mitotic metaphase/anaphase transition | 0.016 |
| regulation of nucleotide-excision repair | 0.021 |
| structural constituent of cytoskeleton | 0.007 |
Mildly Chaotic
| GeneSet | p-value |
|---|---|
| calcium ion binding | 0.002 |
| inflammatory response | 0.032 |
| mRNA splicing, via spliceosome | 0.011 |
| negative regulation of transcription by RNA polymerase II | 0.020 |
Strongly Chaotic
| GeneSet | p-value |
|---|---|
| enzyme binding | 0.015 |
| positive regulation of angiogenesis | 0.023 |
Significant KEGG Pathways (Complexity)
Gained Complexity
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Dilated cardiomyopathy | 0.016 | |
| Leukocyte transendothelial migration | 0.009 | |
| Small cell lung cancer | 0.468 | ✅ |
Lost Complexity
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Pathways in cancer | 0.250 | ✅ |
| Regulation of actin cytoskeleton | 0.016 |
Significant KEGG Pathways (Spectral Entropy)
Strongly Anti-Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Alzheimer disease | 0.000 |
Mildly Chaotic
| GeneSet | p-value | Cancer Pathway |
|---|---|---|
| Pathways in cancer | 1.000 | ✅ |
| Small cell lung cancer | 1.000 | ✅ |
Significant HALLMARK Genes (Complexity)
Gained Complexity
| GeneSet | p-value |
|---|---|
| HALLMARK_IL2_STAT5_SIGNALING | 0.024 |
Significant HALLMARK Genes (Spectral Entropy)
Mildly Anti-Chaotic
| GeneSet | p-value |
|---|---|
| HALLMARK_IL2_STAT5_SIGNALING | 0.023 |