Data set name: GSE2379

Brief description:

The prognosis of hypopharyngeal cancers is influenced by many known factors (TNM staging and grading of differentiation). However, these factors are not sufficient to predict the outcome, so new markers are needed that would be able to stage patients in prognostic groups. This is the problem addressed in our second classification model of this data set. Namely, we are trying to distinguish between normal tissue (N), early tumors (E_T) and late tumors that are additionally subdivided into three subtypes according to clinical behavior 3 years or more after surgery: patients who did not (NM) or did (M) develop metastases, or had local recurrence (LR) within 3 years.

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

Diagnostic classes:

- late tumor without metastases (T_NM): 11 examples (28.9%)

- normal tissue (N): 4 examples (10.5%)

- early tumor (T_E): 4 examples (10.5%)

- late tumor with local recurrence (T_LR): 4 examples (10.5%)

- late tumor with metastases (T_M): 15 examples (39.5%)

Predictive accuracy with 10-fold cross validation (classifying using the best projection with eight attributes):

Classification accuracy: 38.33%

Area under curve (AUC): 0.602

	Score: 85.12% Genes: 1364_at: protein tyrosine phosphatase, receptor-type, Z polypeptide 1, PTPRZ1 37632_s_at: zuotin related factor 1, ZRF1 36569_at: C-type lectin domain family 3, member B, CLEC3B 37762_at: epithelial membrane protein 1, EMP1 218_at: IK cytokine, down-regulator of HLA II, IK 32849_at: SMC1 structural maintenance of chromosomes 1-like 1 (yeast), SMC1L1 32378_at: pyruvate kinase, muscle, PKM2 38922_at: tyrosine kinase, non-receptor, 1, TNK1
	Score: 96.39% Genes: 35463_at: homeo box (expressed in ES cells) 1, HESX1 160031_at: cadherin 3, type 1, P-cadherin (placental), CDH3 38922_at: tyrosine kinase, non-receptor, 1, TNK1 948_s_at: peptidylprolyl isomerase D (cyclophilin D), PPID 37600_at: extracellular matrix protein 1, ECM1 36345_g_at: coagulation factor II (thrombin) receptor-like 1, F2RL1
	Score: 64.29% Genes: 37632_s_at: zuotin related factor 1, ZRF1 36890_at: periplakin, PPL 37171_at: kinesin family member 23, KIF23 218_at: IK cytokine, down-regulator of HLA II, IK

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: 38922_at: tyrosine kinase, non-receptor, 1, TNK1 38302_at: zinc finger protein 202, ZNF202 37632_s_at: zuotin related factor 1, ZRF1 218_at: IK cytokine, down-regulator of HLA II, IK 37762_at: epithelial membrane protein 1, EMP1 37985_at: lamin B1, LMNB1 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 36890_at: periplakin, PPL 37939_at: apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C, APOBEC3C 35749_at: transcriptional adaptor 3 (NGG1 homolog, yeast)-like, TADA3L 36345_g_at: coagulation factor II (thrombin) receptor-like 1, F2RL1 36569_at: C-type lectin domain family 3, member B, CLEC3B 910_at: thymidine kinase 1, soluble, TK1 32378_at: pyruvate kinase, muscle, PKM2 1364_at: protein tyrosine phosphatase, receptor-type, Z polypeptide 1, PTPRZ1 32520_at: thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian) /// nuclear receptor subfamily 1, group D, member 1, THRA /// NR1D1 38190_r_at: DEP domain containing 5, DEPDC5 32868_at: transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase), TGM3 1772_s_at: farnesyltransferase, CAAX box, alpha, FNTA 37171_at: kinesin family member 23, KIF23