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Sebastiani, P, Ramoni, M and Kohane IS. Bayesian Analysis of Differential Gene Expression. Under review. |
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The paper describing the method and its application to the analysis of differential gene expression experiments. |
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Sebastiani, P, Ramoni, M and Kohane IS. Bayesian Analysis of Differential Gene Expression. 2002. [PDF]
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Slides from the overview presentation of the method and its application to the analysis of differential gene expression. |
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Analysis results of the publicly available prostate cancer dataset described in D. Singh et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell, 1:203209, 2002. Expression profiles were collected using the U95Av2 Affymetrix microarray. We analysed the original images files (.cel) with the newest Affymetrix software MAS 5.0.
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Molecular classification |
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Objective: Identify molecular profiles of prostate cancer cells versus normal cells. |
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Materials: Expression profiles derived from 102 prostatectomy specimens from patients undergoing surgery between 1996 and 1997. Fifty samples are from nontumor prostate specimens, and 52 are from with prostate cancer specimens. |
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Results: 97% predictive accuracy [WWW]
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Outcome prediction |
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Objective: identify a molecular profile able to discriminate between patients at risk of relapsing and those who are not. |
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Materials: Expression profiles derived from 21 tumor prostatectomy specimens. Thirteen samples are from patients having remained relapse free for at least four years after the surgery and eight samples are from patients having relapsed. |
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Results: 100% predictive accuracy [WWW]
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Molecular Signature of Gleason Score |
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Objective: Correlate gene expression profiles with Gleason Score. |
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Materials: Expression profiles derived from 46 tumor prostatectomy samples: 26 samples were assigned a Gleason Score 6, whereas 20 samples were assigned a Gleason Score 7.
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Results: 100% predictive accuracy [WWW]
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Molecular Signature of Capsular Penetration |
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Objective: Correlate gene expression profiles with capsular penetration. |
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Materials: Expression profiles derived from 49 tumor prostatectomy samples: 29 samples with negative capsular penetration, whereas 20 samples had positive capsular penetration.
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Results: 94% predictive accuracy [WWW]
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Molecular Signature of Positive Surgical Margins |
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Objective: Correlate gene expression profiles with positive surgical margins. |
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Materials: Expression profiles derived from 52 tumor prostatectomy samples. Thirty eight samples with no positive surgical margin, whereas 14 samples had positive surgical margins. |
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Results: 98% predictive accuracy [WWW]
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