Analysis of Molecular and Clinical Data at PolyomX
- Jennifer Listgarten
- Russ Greiner, Dept of Computing Science; PI of AICML
- Adrian Driga
- Kathryn Graham
- Sambasivarao Damaraju, Cross Cancer Institute
- John Mackey, Cross Cancer Institute
- Carol Cass, Cross Cancer Institute
PolyomX has conducted several population-based association studies on gene expression microarray and SNP type data to determine the contribution of genes to disease susceptibility and clinical characteristics. For each study, we have generated datasets for investigation from the DORA database and have analyzed the data using software tools that have been developed by PolyomX or are publicly available to researchers. The data analysis process can be automated so that researchers can easily generate result reports for various combinations of parameters and datasets.We present the analysis process for gene expression microarray data, focusing on prediction of clinical characteristics and survival analysis, and describe each step of the process from data generation to results. We use a real dataset in which the identity of the breast cancer patients has been anonymized, and we list the genes that are differentially expressed between the classes defined by Nuclear Grade and ER status. We include the results generated using a software package, BRB ArrayTools, available from the National Cancer Institute (US). We also give details on how one would interpret the results of the data analysis.
Citation
J. Listgarten, R. Greiner, A. Driga, K. Graham, S. Damaraju, J. Mackey, C. Cass. "Analysis of Molecular and Clinical Data at PolyomX". ACB Annual Research Meeting, Banff, November 2004.| Keywords: | medical informatics, PolyomX, machine learning |
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BibTeX
@incollection{Listgarten+al:ACBAnnualMeeting04,
author = {Jennifer Listgarten and Russ Greiner and Adrian Driga and Kathryn
Graham and Sambasivarao Damaraju and John Mackey and Carol Cass},
title = {Analysis of Molecular and Clinical Data at PolyomX},
booktitle = {ACB Annual Research Meeting, Banff},
year = 2004,
}Last Updated: May 30, 2007Submitted by Staurt H. Johnson
