22  Comparison Report: GC/LBCL

Author

Ali Al-Timimi

  • Cancer Category: lymphomas
  • Chip hu35ksuba: 1243 filtered probes
  • Chip hu6800: NA filtered probes

Overall Complexity & Entropy Assessment

Measure All Filtered Probes GO MF Terms KEGG Pathways HALLMARK Genes
Complexity strong loss (uncertain) () strong gain (uncertain) strong loss (moderately supported)
Shannon Entropy no clear change (uncertain) () mildly chaotic (uncertain) no clear change (well supported)
Spectral Entropy no clear change (uncertain) () no clear change (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
9 1 0.021 chromatin remodeling
* 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
7 2 0.012 adaptive immune response; immune response
15 1 0.029 ubiquitin-dependent protein catabolic process
44 1 0.044 positive regulation of protein kinase B signaling
12 2 0.366 RNA processing; RNA splicing
2 2 0.860 protein polyubiquitination; protein ubiquitination
* 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
chromatin remodeling 0.021

Lost Complexity

GeneSet p-value
cadherin binding 0.022
immune response 0.009
integrin-mediated signaling pathway 0.018
positive regulation of protein kinase B signaling 0.044
ubiquitin-dependent protein catabolic process 0.029

Significant GO Molecular Function Terms (Spectral Entropy)

Mildly Anti-Chaotic

GeneSet p-value
proteolysis 0.019

Neutral

GeneSet p-value
adaptive immune response 0.033
cell-cell signaling 0.047
inflammatory response 0.005

Mildly Chaotic

GeneSet p-value
DNA binding 0.007
RNA processing 0.027
apoptotic process 0.031
cell population proliferation 0.006
immune response 0.001
positive regulation of cell population proliferation 0.036
protein heterodimerization activity 0.034
protein phosphorylation 0.033
protein ubiquitination 0.048

Significant KEGG Pathways (Complexity)

⚠️ Plot not available.

Lost Complexity

GeneSet p-value Cancer Pathway
Pathways in cancer 0.254 ✅

Significant KEGG Pathways (Spectral Entropy)

⚠️ Plot not available.

Neutral

GeneSet p-value Cancer Pathway
Pathways in cancer 1.000 ✅

Significant HALLMARK Genes (Complexity)

Lost Complexity

GeneSet p-value
HALLMARK_MITOTIC_SPINDLE 0.003
HALLMARK_MYC_TARGETS_V1 0.020

Significant HALLMARK Genes (Spectral Entropy)

Strongly Chaotic

GeneSet p-value
HALLMARK_IL2_STAT5_SIGNALING 0.026
HALLMARK_MTORC1_SIGNALING 0.026