multiple examples of tumor tissue (public data from whitehead/mit) svm classification of multiple...

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Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining Actual\Predicted BR PR LU CO LY BL ML UT LE RE PA OV MS BR BREAST-BR 1 1 PROSTATE-PR 1 1 LUNG-LU 1 2 COLON-CO 3 LYMPHOM A-LY 6 BLADDER-BL 1 2 M ELANOM A-M L 1 1 UTERUS-UT 2 LEUKEMIA-LE 1 5 RENAL-RE 3 PANCREAS-PA 1 2 OVARY-OV 1 2 M ESOTHELIOM A- MS 3 BRAIN-BR 4 78.25% accuracy Green=Correct Red=Errors We feed multiple cancer types data into the Oracle DB: 16,063 genes, 144 cancer patients. We mine the data using Support Vector Machines and create the confusion matrix

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Page 1: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Multiple Examples of tumor tissue (public data from Whitehead/MIT)

SVM Classification of Multiple Tumor Types

DNA Microarray Data

Oracle Data Mining

Actual\Predicted BR PR LU CO LY BL ML UT LE RE PA OV MS BR

BREAST-BR 1 1 PROSTATE-PR 1 1 LUNG-LU 1 2 COLON-CO 3 LYMPHOMA-LY 6 BLADDER-BL 1 2 MELANOMA-ML 1 1 UTERUS-UT 2 LEUKEMIA-LE 1 5 RENAL-RE 3 PANCREAS-PA 1 2 OVARY-OV 1 2 MESOTHELIOMA-MS

3

BRAIN-BR 4

78.25% accuracy

Green=Correct Red=Errors

We feed multiple cancer types data into the Oracle DB: 16,063 genes, 144 cancer

patients.

We mine the data using Support Vector Machines and create the confusion matrix

Page 2: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

SVM Classification of Multiple Tumor Types

Actual\Predicted BR PR LU CO LY BL ML UT LE RE PA OV MS BR

BREAST-BR 1 1 PROSTATE-PR 1 1 LUNG-LU 1 2 COLON-CO 3 LYMPHOMA-LY 6 BLADDER-BL 1 2 MELANOMA-ML 1 1 UTERUS-UT 2 LEUKEMIA-LE 1 5 RENAL-RE 3 PANCREAS-PA 1 2 OVARY-OV 1 2 MESOTHELIOMA-MS

3

BRAIN-BR 4

78.25% accuracy

Green=Correct Red=Errors

Oracle Data Mining’s SVM models are able to accurately predict the multi-class tumor problem with

78.25% accuracy.

Page 3: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Identify Biomarkers for DLBC Lymphoma Treatment Outcome

Attribute Importance identifies genes correlated with Lymphoma cancer.

Page 4: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Find a Cure for Lymphoma

Literature search on Lymphoma Set up a project workspace Set up a meeting Check lab protocols Store cell histology images Analyze gene expression results Study the markers Find a lead

Page 5: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Study the Markers

Statistical analysis Protein sequence analysis (Swissprot) BLAST Search Protein secondary structure study Search of genes and genetic disorders (OMIM) Pathway modeling

Page 6: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Data Analysis with JDeveloper

Page 7: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Data Analysis with JDeveloper

Page 8: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

PKC Distribution Difference

Page 9: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Statistical Analysis

Create an External Table to read data from lymphoma.txt.

Page 10: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Page 11: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Statistical Analysis

Calculate Mean and Standard Deviation

The t-test shows that the PKC expression levels in cured and fatal patients are significantly different.

Page 12: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Protein sequence analysis Load SwissProt into Oracle XML DB

Load SwissProt into XML DB to learn more about expressed genes of interest

Page 13: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Load SwissProt into XML DB

FTP SwissProt data and schema into Oracle XML DB

Page 14: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Load SwissProt into XML DB

Access XML schema using XML Spy (XML editor) which connects to the database using WebDAV

Page 15: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Load SwissProt into XML DB

Page 16: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Register the XML Schema

Once schema is registered, XML DB automatically generates tables

Page 17: Multiple Examples of tumor tissue (public data from Whitehead/MIT) SVM Classification of Multiple Tumor Types DNA Microarray Data Oracle Data Mining 78.25%

Describe the Table Generated

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