Metabolic module mining based on independent component analysis in arabidopsis thaliana

Xiao Han, Cong Chen, Tae Kyung Hyun, Ritesh Kumar, Jae Yean Kim

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Independent Component Analysis (ICA) has been introduced as one of the useful tools for gene-functional discovery in animals. However, this approach has been poorly utilized in the plant sciences. In the present study, we have exploited ICA combined with pathway enrichment analysis to address the statistical challenges associated with genome-wide analysis in plant system. To generate an Arabidopsis metabolic platform, we collected 4,373 Affymetrix ATH1 microarray datasets. Out of the 3,232 metabolic genes and transcription factors, 99.47% of these genes were identified in at least one component, indicating the coverage of most of the metabolic pathways by the components. During the metabolic pathway enrichment analysis, we found components that indicate an independent regulation between the isoprenoid biosynthesis pathways. We also utilized this analysis tool to investigate some transcription factors involved in secondary cell wall biogenesis. This approach has identified remarkably more transcription factors compared to previously reported analysis tools. A website providing user-friendly searching and downloading of the entire dataset analyzed by ICA is available at ICA combined with pathway enrichment analysis might provide a powerful approach for the extraction of the components responsible for a biological process of interest in plant systems.

Original languageEnglish (US)
Pages (from-to)295-304
Number of pages10
JournalMolecules and cells
Issue number3
StatePublished - Sep 2012
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the World Class University program (grant R33-10002) through the National Research Foundation of Korea, which is funded by the Ministry of Education, Science and Technology, and by a grant from the Next-Generation BioGreen 21 Program (SSAC, grant PJ008109), Rural Development Administration, Republic of Korea.


  • Independent component analysis (ICA)
  • Isoprenoid biosynthesis pathway
  • Lignin biosynthesis pathway
  • Secondary cell wall biogenesis
  • Transcription factor (TF)


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