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Biological Data Analysis Laboratories

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Abstract

The Biological Data Analysis Laboratories at IUSCC and Purdue University

imageProcessed samples will undergo lipidomic, oxidative stress, and SNP analysis at the IU Simon Cancer Center and global proteomic, glycoproteomic and metabolomic analysis at Purdue University.

These analyses are a major focus of the CCE project. They will serve as the basis for the statistical modeling that will provide the molecular signatures to be rapidly tested in the IUSCC clinics, identifying those that can accurately predict CRC susceptibility and treatment outcomes for diagnosed CRC patients.

We will integrate OMIC data from four disparate datasets: Genomic (SNP), Biological assays, Mass Spectrometry (MS), and Nuclear Magnetic Resonance (NMR). While the data integration effort will be a significant challenge, the integration is also the great promise of the CCE project.

The power of the iterative approach we propose is that

  • More patient and control data will continually be accrued and added to the CCE system
  • Novel technologies to generate additional OMIC data will continue to emerge and will be rapidly applied
  • As additional data is supplied to the system, models will continue to improve in their predictive ability.

Cite this work

Researchers should cite this work as follows:

  • (2008), "Biological Data Analysis Laboratories," http://ccehub.org/resources/103.

Tags

  1. biomarker discovery 13
  2. colorectal cancer 25
  3. global proteomics 10
  4. glycoproteomics 4
  5. lipidomics 7
  6. metabolomics 12
  7. OMIC analysis 27
  8. oxidative stress 4

In This Series

  1. OMIC Data Formats: Notes for the Modeling Research Group

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    20 Feb 2009 | Notes | Contributor(s): Ann Christine Catlin

    Each OMIC analysis laboratory has one or more analysis workflows that begin with instrument-generated datasets, where the format of the instrument dataset made available to modeling researchers for analysis depends on the instrument, the analysis mode, and the available file conversion …

  2. Klaunig Oxidative Stress Analysis Laboratory

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    07 Feb 2009 | Series | Contributor(s): James E. Klaunig, Ph.D.,

    Studies in the laboratory of James Klaunig concentrate on understanding the mechanism by which chemicals induce cancer and the means to prevent or retard this process. Recent investigations have revolved around the role of oxidative stress and oxidative damage in the induction of cancer by …

  3. Regnier Glycoproteomics Analysis Laboratory

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    07 Feb 2009 | Series | Contributor(s): wonryeon cho, Ann Christine Catlin

    While entire proteome approaches for biomarker discovery have held great promise for biomarker discovery, significant challenges have arisen in their use. The most significant is that ten proteins make up ninety percent of plasma, and removal of these proteins is costly and only marginally improves …

  4. Global Proteomics Analysis Laboratory

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    07 Feb 2009 | Series | Contributor(s): Ann Christine Catlin

    The proteomic and metabolomic laboratory at Purdue University's Bindley Bioscience Center performs global proteomics analysis for the CCE project. The facility uses proteomic and metabolomic tools to evaluate biological problems such as oxidative stress and apoptosis, cancer, aging and …

  5. Teegarden Laboratory for Vitamin D Analysis

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    07 Feb 2009 | Series | Contributor(s): Dorothy Teegarden, James E. Klaunig, Ph.D., Bo Xie

    Studies in the laboratory of Dorothy Teegarden focus on Vitamin D, which is associated with a reduced incidence of several cancers, including prostate, colon and breast cancer. Dr. Teegarden is investigating the role and the mechanism of Vitamin D metabolites in the growth of cells and programmed …

  6. Raftery Metabolomics Analysis Laboratory

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    07 Feb 2009 | Series | Contributor(s): Daniel Raftery, Lingyan Liu

    The Raftery Group is led by Professor M. Daniel Raftery of Purdue University's Department of Chemistry. Their research focuses on the development and application of advanced methods in metabolomics and bioanalytical NMR spectroscopy. Professor Raftery's laboratory utilizes the latest technological …

  7. Xu Lipidomics Analysis Laboratory

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    14 Oct 2008 | Series | Contributor(s): , HUI CAI

    The lipidomic approach in the laboratory of Yan Xu deals with understanding, at the molecular level, the mechanism of development of ovarian, breast, prostate, and other malignancies. These include developing effective diagnostic and prognostic biomarkers for these diseases and novel therapeutic …

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