Plant photosynthesis phenomics data quality control

Lei Xu, Jeffrey A. Cruz, Linda J. Savage, David M. Kramer, Jin Chen

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Motivation: Plant phenomics, the collection of large-scale plant phenotype data, is growing exponentially. The resources have become essential component of modern plant science. Such complex datasets are critical for understanding the mechanisms governing energy intake and storage in plants, and this is essential for improving crop productivity. However, a major issue facing these efforts is the determination of the quality of phenotypic data. Automated methods are needed to identify and characterize alterations caused by system errors, all of which are difficult to remove in the data collection step and distinguish them from more interesting cases of altered biological responses. Results: As a step towards solving this problem, we have developed a coarse-to-refined model called dynamic filter to identify abnormalities in plant photosynthesis phenotype data by comparing light responses of photosynthesis using a simplified kinetic model of photosynthesis. Dynamic filter employs an expectation-maximization process to adjust the kinetic model in coarse and refined regions to identify both abnormalities and biological outliers. The experimental results show that our algorithm can effectively identify most of the abnormalities in both real and synthetic datasets. Availability and implementation: Software available at www.msu.edu/%7Ejinchen/DynamicFilter.

Original languageEnglish
Pages (from-to)1796-1804
Number of pages9
JournalBioinformatics
Volume31
Issue number11
DOIs
StatePublished - Jun 1 2015

Bibliographical note

Publisher Copyright:
© The Author 2015. Published by Oxford University Press. All rights reserved.

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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