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Data set name: GSE2685


Original data set (GSE2685)
Data set for Orange
Brief description:
For this data set we induced models for two different classification problems. With the first model we are trying to distinguish between diffuse and intestinal tumor gastric samples and normal gastric tissue.

Platform: Affymetrix GeneChip Human Full Length Array HuGeneFL

Diagnostic classes:
- normal gastric tissue (Normal): 8 examples (26.7%)
- diffuse gastric tumor (Diffuse): 5 examples (16.7%)
- intestinal gastric tumor (Intestinal): 17 examples (56.7%)
Number of genes: 4522
Number of samples: 30
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: 60.00%
Area under curve (AUC): 0.762
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: 99.57%
Genes:
D26129_at: ribonuclease, RNase A family, 1 (pancreatic), RNASE1
U66052_at: Iduronate 2-sulfatase (Hunter syndrome), IDS
X83416_s_at: prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia), PRNP
U46006_s_at: cysteine and glycine-rich protein 2, CSRP2
U03105_at: proline-rich nuclear receptor coactivator 1, PNRC1
U50360_s_at: calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma, CAMK2G
X81817_at: B-cell receptor-associated protein 31, BCAP31
U07969_s_at: cadherin 17, LI cadherin (liver-intestine), CDH17
Score: 98.99%
Genes:
M62628_s_at: Hypothetical protein MGC27165, MGC27165
D87742_at: C219-reactive peptide /// AAAP6077 /// similar to C219-reactive peptide, KIAA0268 /// UNQ6077 /// LOC440751
U86755_s_at: a disintegrin and metalloproteinase domain 17 (tumor necrosis factor, alpha, converting enzyme), ADAM17
U03105_at: proline-rich nuclear receptor coactivator 1, PNRC1
U95040_at: tripartite motif-containing 28, TRIM28
D78132_s_at: Ras homolog enriched in brain, RHEB
Score: 95.38%
Genes:
AC002077_at: guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1, GNAT1
X05409_at: aldehyde dehydrogenase 2 family (mitochondrial), ALDH2
X83416_s_at: prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia), PRNP
U26424_at: serine/threonine kinase 3 (STE20 homolog, yeast), STK3

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:
X83416_s_at: prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia), PRNP
U26424_at: serine/threonine kinase 3 (STE20 homolog, yeast), STK3
X05409_at: aldehyde dehydrogenase 2 family (mitochondrial), ALDH2
M62628_s_at: Hypothetical protein MGC27165, MGC27165
U21931_at: fructose-1,6-bisphosphatase 1, FBP1
X81817_at: B-cell receptor-associated protein 31, BCAP31
D26129_at: ribonuclease, RNase A family, 1 (pancreatic), RNASE1
U03105_at: proline-rich nuclear receptor coactivator 1, PNRC1
U86755_s_at: a disintegrin and metalloproteinase domain 17 (tumor necrosis factor, alpha, converting enzyme), ADAM17
S68616_at: solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive), SLC9A1
L41939_at: EPH receptor B2, EPHB2
U66469_at: cell growth regulator with ring finger domain 1, CGRRF1
X66839_at: carbonic anhydrase IX, CA9
U19948_at: protein disulfide isomerase family A, member 2, PDIA2
U70663_at: Kruppel-like factor 4 (gut), KLF4
M63154_at: gastric intrinsic factor (vitamin B synthesis), GIF
U07969_s_at: cadherin 17, LI cadherin (liver-intestine), CDH17
AC002077_at: guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1, GNAT1
V00572_at: phosphoglycerate kinase 1, PGK1
X96752_at: L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain, HADHSC