Data set name: braintumor

Brief description:

We built a classification model that attempts to distinguishes between different embryonal tumors of the central nervous system on the basis of DNA expression signatures. We used the dataset A1 from the original research done by Pomeroy et al., consisting of 40 samples from 5 diagnostic classes (medulloblastomas, malignant gliomas, atypicalteratoid/rhabdoid tumors, primitive neuroectodermal tumors and normal cerebella).

Platform: Affymetrix HuGeneFL array

Diagnostic classes:

- medulloblastoma (medulloblastoma): 10 examples (25.0%)

- malignant glioma (glioma): 10 examples (25.0%)

- Rhabdoid tumor (RhabdoidTu): 10 examples (25.0%)

- normal cerebellum (Normal): 4 examples (10.0%)

- primitive neuroectodermal tumor (PNET): 6 examples (15.0%)

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

Classification accuracy: 52.50%

Area under curve (AUC): 0.837

	Score: 95.31% Genes: U44060_at: prospero-related homeobox 1, PROX1 M30448_s_at: fibrillarin, FBL X13916_at: low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor), LRP1 M93426_at: "protein tyrosine phosphatase, receptor-type, Z polypeptide 1", PTPRZ1 D87463_at: phytanoyl-CoA hydroxylase interacting protein, PHYHIP M12125_at: tropomyosin 2 (beta), TPM2 J04164_at: interferon induced transmembrane protein 1 (9-27), IFITM1 M80397_s_at: "polymerase (DNA directed), delta 1, catalytic subunit 125kDa", POLD1
	Score: 91.26% Genes: M93119_at: insulinoma-associated 1, INSM1 D26070_at: "inositol 1,4,5-triphosphate receptor, type 1", ITPR1 X86693_at: "SPARC-like 1 (mast9, hevin)", SPARCL1 X13916_at: low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor), LRP1 X79683_s_at: "laminin, beta 2 (laminin S)", LAMB2 X14830_at: "cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)", CHRNB1
	Score: 82.26% Genes: M30448_s_at: fibrillarin, FBL M93426_at: "protein tyrosine phosphatase, receptor-type, Z polypeptide 1", PTPRZ1 M12125_at: tropomyosin 2 (beta), TPM2 D87463_at: phytanoyl-CoA hydroxylase interacting protein, PHYHIP

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: M93119_at: insulinoma-associated 1, INSM1 M12125_at: tropomyosin 2 (beta), TPM2 X86693_at: "SPARC-like 1 (mast9, hevin)", SPARCL1 U90902_at: T-cell lymphoma invasion and metastasis 1, TIAM1 U14968_at: ribosomal protein L27a, RPL27A D26070_at: "inositol 1,4,5-triphosphate receptor, type 1", ITPR1 X63578_rna1_at: parvalbumin, PVALB M32304_s_at: TIMP metallopeptidase inhibitor 2, TIMP2 U48250_at: oligodendrocyte lineage transcription factor 2, OLIG2 D87463_at: phytanoyl-CoA hydroxylase interacting protein, PHYHIP X13916_at: low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor), LRP1 U44060_at: prospero-related homeobox 1, PROX1 L35592_at: Similar to expressed sequence AW125688, --- U40372_at: "phosphodiesterase 1C, calmodulin-dependent 70kDa", PDE1C L38969_at: thrombospondin 3, THBS3 M93426_at: "protein tyrosine phosphatase, receptor-type, Z polypeptide 1", PTPRZ1 X79683_s_at: "laminin, beta 2 (laminin S)", LAMB2 Z15108_at: "protein kinase C, zeta", PRKCZ L33243_at: polycystic kidney disease 1 (autosomal dominant), PKD1 J04469_at: "creatine kinase, mitochondrial 1B", CKMT1B