FRI > Biolab > Supplements

Data set name: GSE412


Original data set (GSE412)
Data set for Orange
Brief description:
The data set includes gene expression information on 110 childhood acute lymphoblastic leukemia samples. For this data set we induced models for two different classification problems. With the second model we try to distinguish between childhood acute lymphoblastic leukemia cells based on changes in gene expression after four different treatment types.

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

Diagnostic classes:
- mercaptopurine alone (MP): 13 examples (21.7%)
- high-dose methotrexate (HDMTX): 21 examples (35.0%)
- mercaptopurine and low-dose methotrexate (LDMTX_MP): 16 examples (26.7%)
- mercaptopurine and high-dose methotrexate (HDMTX_MP): 10 examples (16.7%)
Number of genes: 8280
Number of samples: 60
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: 36.67%
Area under curve (AUC): 0.647
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: 69.61%
Genes:
34510_at: DNA replication factor, CDT1
34525_at: T-cell leukemia/lymphoma 1B /// T-cell leukemia/lymphoma 6, TCL1B /// TCL6
31850_at: glutamate-cysteine ligase, catalytic subunit, GCLC
35942_at: GA binding protein transcription factor, beta subunit 2 /// hypothetical protein FLJ10038, GABPB2 /// FLJ10038
35940_at: POU domain, class 4, transcription factor 1, POU4F1
39927_at: Rho GTPase activating protein 5, ARHGAP5
31506_s_at: defensin, alpha 1, myeloid-related sequence /// defensin, alpha 3, neutrophil-specific, DEFA1 /// DEFA3
31793_at: defensin, alpha 3, neutrophil-specific, DEFA3
Score: 66.27%
Genes:
160042_s_at: homeo box B6, HOXB6
33270_i_at: Dmx-like 1, DMXL1
31506_s_at: defensin, alpha 1, myeloid-related sequence /// defensin, alpha 3, neutrophil-specific, DEFA1 /// DEFA3
41471_at: S100 calcium binding protein A9 (calgranulin B), S100A9
33353_at: adenylate cyclase 1 (brain), ADCY1
160022_at: colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog, CSF1R
Score: 65.70%
Genes:
514_at: Cas-Br-M (murine) ecotropic retroviral transforming sequence b, CBLB
31850_at: glutamate-cysteine ligase, catalytic subunit, GCLC
31506_s_at: defensin, alpha 1, myeloid-related sequence /// defensin, alpha 3, neutrophil-specific, DEFA1 /// DEFA3
35169_at: collagen, type XVI, alpha 1, COL16A1

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:
31506_s_at: defensin, alpha 1, myeloid-related sequence /// defensin, alpha 3, neutrophil-specific, DEFA1 /// DEFA3
33876_at: WW domain containing transcription regulator 1, WWTR1
31850_at: glutamate-cysteine ligase, catalytic subunit, GCLC
35158_at: v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian), MYCN
160042_s_at: homeo box B6, HOXB6
35241_at: zinc finger protein 518, ZNF518
34525_at: T-cell leukemia/lymphoma 1B /// T-cell leukemia/lymphoma 6, TCL1B /// TCL6
514_at: Cas-Br-M (murine) ecotropic retroviral transforming sequence b, CBLB
1577_at: androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy disease), AR
160022_at: colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog, CSF1R
947_at: MCM7 minichromosome maintenance deficient 7 (S. cerevisiae), MCM7
37458_at: CDC45 cell division cycle 45-like (S. cerevisiae), CDC45L
1783_at: Ras and Rab interactor 2, RIN2
34510_at: DNA replication factor, CDT1
37781_at: neurexin 2, NRXN2
39927_at: Rho GTPase activating protein 5, ARHGAP5
40589_at: syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2), SNTB2
1206_at: cyclin-dependent kinase 5, CDK5
31793_at: defensin, alpha 3, neutrophil-specific, DEFA3
1462_s_at: polymerase (DNA directed), delta 1, catalytic subunit 125kDa, POLD1