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Data set name: GSE2379


Original data set (GSE2379)
Data set for Orange
Brief description:
For this data set we induced models for two different classification problems. With the first model we are simply trying to distinguish between normal tissue samples from the head and neck region and hypopharyngeal cancer samples.

Platform: Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A

Diagnostic classes:
- hypopharyngeal cancer (T): 34 examples (89.5%)
- normal tissue (N): 4 examples (10.5%)
Number of genes: 9021
Number of samples: 38
Note: From the originally measured 12625 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): 0.691
Following are 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: 100.00%
Genes:
160042_s_at: homeo box B6, HOXB6
160041_at: protein tyrosine phosphatase, non-receptor type 18 (brain-derived), PTPN18
160024_at: cyclin-dependent kinase (CDC2-like) 10, CDK10
160020_at: matrix metalloproteinase 14 (membrane-inserted), MMP14
37762_at: epithelial membrane protein 1, EMP1
38051_at: mal, T-cell differentiation protein, MAL
37920_at: paired-like homeodomain transcription factor 1, PITX1
36569_at: C-type lectin domain family 3, member B, CLEC3B
Score: 100.00%
Genes:
39333_at: collagen, type IV, alpha 1, COL4A1
160044_g_at: aconitase 2, mitochondrial, ACO2
160026_at: protein kinase, X-linked, PRKX
37762_at: epithelial membrane protein 1, EMP1
36890_at: periplakin, PPL
36569_at: C-type lectin domain family 3, member B, CLEC3B
Score: 100.00%
Genes:
160029_at: protein kinase C, beta 1, PRKCB1
160027_s_at: insulin-like growth factor 2 receptor, IGF2R
36890_at: periplakin, PPL
36569_at: C-type lectin domain family 3, member B, CLEC3B

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:
160041_at: protein tyrosine phosphatase, non-receptor type 18 (brain-derived), PTPN18
160027_s_at: insulin-like growth factor 2 receptor, IGF2R
36569_at: C-type lectin domain family 3, member B, CLEC3B
37762_at: epithelial membrane protein 1, EMP1
36290_s_at: fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included) /// fucosyltransferase 5 (alpha (1,3) fucosyltransferase) /// fucosyltransferase 6 (alpha (1,3) fucosyltransferase), FUT3 /// FUT5 /// FUT6
160020_at: matrix metalloproteinase 14 (membrane-inserted), MMP14
36890_at: periplakin, PPL
160033_s_at: X-ray repair complementing defective repair in Chinese hamster cells 1, XRCC1
36289_f_at: fucosyltransferase 6 (alpha (1,3) fucosyltransferase), FUT6
160032_at: interleukin 6 receptor, IL6R
160044_g_at: aconitase 2, mitochondrial, ACO2
32868_at: transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase), TGM3
38098_at: lipin 1, LPIN1
160042_s_at: homeo box B6, HOXB6
160024_at: cyclin-dependent kinase (CDC2-like) 10, CDK10
40315_at: serine protease inhibitor, Kazal type 5, SPINK5
38051_at: mal, T-cell differentiation protein, MAL
37920_at: paired-like homeodomain transcription factor 1, PITX1
160029_at: protein kinase C, beta 1, PRKCB1
31343_at: interleukin 1 receptor antagonist, IL1RN