Data set name: GSE89


Original data set (GSE89)
Data set for Orange
Brief description:
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):
Classification accuracy: 90.00%
Area under curve (AUC): 0.969
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.

Genes:
U90549_at: high mobility group nucleosomal binding domain 4, HMGN4
M55998_s_at: collagen, type I, alpha 1, COL1A1
Z19554_s_at: vimentin, VIM
X13334_at: CD14 antigen, CD14
J04988_at: heat shock 90kDa protein 1, beta, HSPCB
X68561_at: Sp4 transcription factor, SP4
L11566_at: ribosomal protein L18, RPL18
S77393_at: Kruppel-like factor 3 (basic), KLF3
L19872_at: aryl hydrocarbon receptor, AHR
X73460_at: ribosomal protein L3, RPL3
U68485_at: bridging integrator 1, BIN1
X03663_at: colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog, CSF1R
U07231_at: G-rich RNA sequence binding factor 1, GRSF1
M57731_s_at: chemokine (C-X-C motif) ligand 2, CXCL2
X67247_rna1_at: ribosomal protein S8, RPS8
U52696_s_at: cAMP responsive element binding protein-like 1 /// tenascin XB, CREBL1 /// TNXB
L19686_rna1_at: macrophage migration inhibitory factor (glycosylation-inhibiting factor), MIF
X55715_at: ribosomal protein S3, RPS3
U09937_rna1_s_at: plasminogen activator, urokinase receptor, PLAUR
Z49148_s_at: ribosomal protein L29, RPL29