Making Use of Cancer Genomic Databases

Chad J. Creighton1

1 Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 19.14
DOI:  10.1002/cpmb.49
Online Posting Date:  January, 2018
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The vast amounts of genomic data now deposited in public repositories represent rich resources for cancer researchers. Large‐scale genomics initiatives such as The Cancer Genome Atlas have made available data from multiple molecular profiling platforms (e.g., somatic mutation, RNA and protein expression, and DNA methylation) for the same set of over 10,000 human tumors. There has been much collective effort toward providing user‐friendly software tools for biologists lacking computational skills to ask questions of large‐scale genomic datasets. At the same time, there remains a clear need for skilled bioinformatics analysts to answer the types of questions that cannot easily be addressed using the public user‐friendly software tools. This overview introduces the reader to the many resources available for working with cancer genomic databases. © 2018 by John Wiley & Sons, Inc.

Keywords: analysis software; cancer genomics; cancer bioinformatics; databases; The Cancer Genome Atlas (TCGA)

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Table of Contents

  • Introduction
  • Cancer Bioinformatics
  • Levels of Genomic Data
  • Large‐Scale Cancer Genomics Initiatives
  • Cancer Genomic Database Resources
  • Acquiring Bioinformatics Analysis Expertise
  • Concluding Remarks
  • Acknowledgements
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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