Discovering collectively informative descriptors from high-throughput experiments Public Deposited

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Creator
  • Ward, William O
    • Other Affiliation: NHEERL Environmental Carcinogenesis Division, United States Environmental Protection Agency, Research Triangle Park, NC, USA
  • Wright, Fred A.
    • Affiliation: Gillings School of Global Public Health, Department of Biostatistics
  • Jeffries, Clark D
    • Affiliation: Renaissance Computing Institute, Eshelman School of Pharmacy
  • Perkins, Diana
    • Affiliation: School of Medicine, Department of Psychiatry
Abstract
  • Abstract Background Improvements in high-throughput technology and its increasing use have led to the generation of many highly complex datasets that often address similar biological questions. Combining information from these studies can increase the reliability and generalizability of results and also yield new insights that guide future research. Results This paper describes a novel algorithm called BLANKET for symmetric analysis of two experiments that assess informativeness of descriptors. The experiments are required to be related only in that their descriptor sets intersect substantially and their definitions of case and control are consistent. From resulting lists of n descriptors ranked by informativeness, BLANKET determines shortlists of descriptors from each experiment, generally of different lengths p and q. For any pair of shortlists, four numbers are evident: the number of descriptors appearing in both shortlists, in exactly one shortlist, or in neither shortlist. From the associated contingency table, BLANKET computes Right Fisher Exact Test (RFET) values used as scores over a plane of possible pairs of shortlist lengths 12. BLANKET then chooses a pair or pairs with RFET score less than a threshold; the threshold depends upon n and shortlist length limits and represents a quality of intersection achieved by less than 5% of random lists. Conclusions Researchers seek within a universe of descriptors some minimal subset that collectively and efficiently predicts experimental outcomes. Ideally, any smaller subset should be insufficient for reliable prediction and any larger subset should have little additional accuracy. As a method, BLANKET is easy to conceptualize and presents only moderate computational complexity. Many existing databases could be mined using BLANKET to suggest optimal sets of predictive descriptors.
Date of publication
Identifier
  • 20021653
  • doi:10.1186/1471-2105-10-431
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Clark D Jeffries et al.; licensee BioMed Central Ltd.
License
Journal title
  • BMC Bioinformatics
Journal volume
  • 10
Journal issue
  • 1
Page start
  • 431
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2105
Bibliographic citation
  • BMC Bioinformatics. 2009 Dec 18;10(1):431
Access
  • Open Access
Publisher
  • BioMed Central Ltd
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