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Data set name: GSE2685

Original data set (GSE2685)
Data set for Orange

Brief description:: In the second model of the gastric cancer data set (GSE2685) we combined the diffuse and intestinal advanced gastric tumor samples into one class in order to distinguish cancer from noncancerous samples based on gene expression measurements.

Platform: Affymetrix GeneChip Human Full Length Array HuGeneFL

Diagnostic classes:: - Normal gastric tissue (Normal): 8 examples (26.7%); - Advanced gastric cancer tissue (Tumor): 22 examples (73.3%)

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: 93.33%; Area under curve (AUC): 0.915

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: 99.97% Genes: M63154_at: gastric intrinsic factor (vitamin B synthesis), GIF D26129_at: ribonuclease, RNase A family, 1 (pancreatic), RNASE1 D87742_at: C219-reactive peptide /// AAAP6077 /// similar to C219-reactive peptide, KIAA0268 /// UNQ6077 /// LOC440751 S68616_at: solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive), SLC9A1 AB003102_at: proteasome (prosome, macropain) 26S subunit, non-ATPase, 11, PSMD11 M31520_rna1_at U51478_at: ATPase, Na+/K+ transporting, beta 3 polypeptide, ATP1B3 X74801_at: chaperonin containing TCP1, subunit 3 (gamma), CCT3
	Score: 99.97% Genes: X05997_at: lipase, gastric, LIPF D26129_at: ribonuclease, RNase A family, 1 (pancreatic), RNASE1 M63154_at: gastric intrinsic factor (vitamin B synthesis), GIF M86752_at: stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein), STIP1 HG2614-HT2710_at X81817_at: B-cell receptor-associated protein 31, BCAP31
	Score: 99.96% Genes: M12759_at: immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides, IGJ D26129_at: ribonuclease, RNase A family, 1 (pancreatic), RNASE1 M86752_at: stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein), STIP1 HG2614-HT2710_at

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:
D26129_at: ribonuclease, RNase A family, 1 (pancreatic), RNASE1
M86752_at: stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein), STIP1
U51478_at: ATPase, Na+/K+ transporting, beta 3 polypeptide, ATP1B3
X96752_at: L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain, HADHSC
U70663_at: Kruppel-like factor 4 (gut), KLF4
AB003102_at: proteasome (prosome, macropain) 26S subunit, non-ATPase, 11, PSMD11
X81817_at: B-cell receptor-associated protein 31, BCAP31
D87742_at: C219-reactive peptide /// AAAP6077 /// similar to C219-reactive peptide, KIAA0268 /// UNQ6077 /// LOC440751
U61397_s_at: SMT3 suppressor of mif two 3 homolog 1 (yeast), SUMO1
M63154_at: gastric intrinsic factor (vitamin B synthesis), GIF
M95178_at: actinin, alpha 1, ACTN1
M12759_at: immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides, IGJ
U21931_at: fructose-1,6-bisphosphatase 1, FBP1
U66052_at: Iduronate 2-sulfatase (Hunter syndrome), IDS
S68616_at: solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive), SLC9A1
L17131_rna1_at: high mobility group AT-hook 1, HMGA1
X74801_at: chaperonin containing TCP1, subunit 3 (gamma), CCT3
X05997_at: lipase, gastric, LIPF
M93425_at: protein tyrosine phosphatase, non-receptor type 12, PTPN12
M31520_rna1_at