Gene Expression Model Selector
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Copyright, © 2003-2005,
Alexander Statnikov,
Constantin F. Aliferis,
Ioannis Tsamardinos,
Discovery Systems Laboratory,
Department of Biomedical Informatics,
Vanderbilt University, Nashville, TN, USA
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Publications
A. Statnikov, I. Tsamardinos, Y. Dosbayev, C.F. Aliferis, "GEMS: A System for Automated Cancer Diagnosis and Biomarker Discovery from Microarray Gene Expression Data",
International Journal of Medical Informatics, 2005 Aug;74(7-8):491-503.
[Pubmed]
A. Statnikov, C.F. Aliferis, I. Tsamardinos, D. Hardin, S. Levy. "
A Comprehensive Evaluation of Multicategory Classification Methods for Microarray Gene Expression Cancer Diagnosis", Bioinformatics, 2005 Mar 1;21(5):631-43
[Pubmed]
[Appendix]
A. Statnikov, C.F. Aliferis, I. Tsamardinos. "Methods for Multi-Category Cancer Diagnosis from Gene Expression Data: A Comprehensive Evaluation to Inform Decision Support System Development",
Medinfo, 2004;2004:813-7
[Article]
[Appendix]
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Datasets used for evaluation
| Dataset name |
Diagnostic Task |
PubMed link |
File |
| 11_Tumors |
11 various human tumor types |
[PubMed] |
11_Tumors.mat (8,520kb)
11_Tumors.txt (1kb)
For use with GEMS: 11_Tumors_GEMS.txt (?kb) |
| 14_Tumors |
14 various human tumor types and 12 normal tissue types |
[PubMed] |
14_Tumors.mat (36,118kb)
14_Tumors.txt (1kb)
For use with GEMS: 14_Tumors_GEMS.txt (?kb) |
| 9_Tumors |
9 various human tumor types |
[PubMed] |
9_Tumors.mat (672kb)
9_Tumors.txt (1kb)
For use with GEMS: 9_Tumors_GEMS.txt (?kb) |
| Brain_Tumor1 |
5 human brain tumor types |
[PubMed] |
Brain_Tumor1.mat (2,082kb)
Brain_Tumor1.txt (1kb)
For use with GEMS: Brain_Tumor1_GEMS.txt (?kb) |
| Brain_Tumor2 |
4 malignant glioma types |
[PubMed] |
Brain_Tumor2.mat (4,051kb)
Brain_Tumor2.txt (1kb)
For use with GEMS: Brain_Tumor2_GEMS.txt (?kb) |
| Leukemia1 |
Acute myelogenous leukemia (AML), acute lympboblastic leukemia (ALL) B-cell, and ALL T-cell |
[PubMed] |
Leukemia1.mat (1,499kb)
Leukemia1.txt (1kb)
For use with GEMS: Leukemia1_GEMS.txt (?kb) |
| Leukemia2 |
AML, ALL, and mixed-lineage leukemia (MLL) |
[PubMed] |
Leukemia2.mat (6,315kb)
Leukemia2.txt (1kb)
For use with GEMS: Leukemia2_GEMS.txt (?kb) |
| Lung_Cancer |
4 lung cancer types and normal tissues |
[PubMed] |
Lung_Cancer.mat (19,985kb)
Lung_Cancer.txt (1kb)
For use with GEMS: Lung_Cancer_GEMS.txt (?kb) |
| SRBCT |
Small, round blue cell tumors (SRBCT) of childhood |
[PubMed] |
SRBCT.mat (1,498kb)
SRBCT.txt (1kb)
For use with GEMS: SRBCT_GEMS.txt (?kb) |
| Prostate_Tumor |
Prostate tumor and normal tissues |
[PubMed] |
Prostate_Tumor.mat (8,376kb)
Prostate_Tumor.txt (1kb)
For use with GEMS: Prostate_Tumor_GEMS.txt (?kb) |
| DLBCL |
Diffuse large b-cell lymphomas (DLBCL) and follicular lymphomas |
[PubMed] |
DLBCL.mat (1,646kb)
DLBCL.txt (1kb)
For use with GEMS: DLBCL_Tumor_GEMS.txt (?kb) |
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Datasets are distributed as Matlab data files (.mat).
Each file contains a matrix with columns corresponding to diagosis (1st column) and genes, and rows corresponding to samples.
The encoding of diagnosis (1st column) is provided in .txt file.
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