The stage of bladder carcinoma at diagnosis is important in determining the disease course of a patient. Based on gene expression values we tried to distinguish between 40 well characterized bladder tumor samples.
Platform: Affymetrix GeneChip Human Full Length Array HuGeneFL
Diagnostic classes:
- tumor stage T2-T4 (T2+): 10 examples (25.0%)
- tumor stage Ta (Ta): 19 examples (47.5%)
- tumor stage T1 (T1): 11 examples (27.5%)
Number of genes: 5724 Number of samples: 40 Note: From the originally measured 7128 probe sets we removed genes that were not present (P) in at least one sample
Predictive accuracy with 10-fold cross validation (classifying using the best projection with eight attributes):
Following are the three best-ranked visualization with eight, six and four attributes in respect to the visualization score, that is, visualizations where examples from different diagnostic classes are best separated:
Score: 99.93% Genes: Z19554_s_at: vimentin, VIM M57731_s_at: chemokine (C-X-C motif) ligand 2, CXCL2 M55998_s_at: collagen, type I, alpha 1, COL1A1 U90549_at: high mobility group nucleosomal binding domain 4, HMGN4 U07231_at: G-rich RNA sequence binding factor 1, GRSF1 U19765_at: zinc finger protein 9 (a cellular retroviral nucleic acid binding protein), ZNF9 L19686_rna1_at: macrophage migration inhibitory factor (glycosylation-inhibiting factor), MIF X68561_at: Sp4 transcription factor, SP4
Score: 99.70% Genes: Z19554_s_at: vimentin, VIM M55998_s_at: collagen, type I, alpha 1, COL1A1 U90549_at: high mobility group nucleosomal binding domain 4, HMGN4 S77393_at: Kruppel-like factor 3 (basic), KLF3 L19686_rna1_at: macrophage migration inhibitory factor (glycosylation-inhibiting factor), MIF X68561_at: Sp4 transcription factor, SP4
Score: 98.91% Genes: Z19554_s_at: vimentin, VIM X03663_at: colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog, CSF1R U90549_at: high mobility group nucleosomal binding domain 4, HMGN4 X67247_rna1_at: ribosomal protein S8, RPS8
Attribute ranking
Following is the histogram of genes showing how often are they present in one of the top 100 radviz visualizations with 8 attributes.