Fuzzy clustering of CPP family in plants with evolution and interaction analyses

Tao Lu, Yongchao Dou, Chi Zhang

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Background: Transcription factors have been studied intensively because they play an important role in gene expression regulation. However, the transcription factors in the CPP family (cystein-rich polycomb-like protein), compared with other transcription factor families, have not received sufficient attention, despite their wide prevalence in a broad spectrum of species, from plants to animals. The total number of known CPP transcription factors in plants is 111 from 16 plants, but only 2 of them have been studied so far, namely TSO1 and CPP1 in Arabidopsis thaliana and soybean, respectively.Methods: In this work, to study their functions, we applied the fuzzy clustering method to all plant CPP transcription factors. The feature vector of each protein sequence for the fuzzy clustering method is encoded by the short length peptides and the combination of functional domain models.Results and conclusions: With the fuzzy clustering method, all plant CPP transcription factors are grouped into two subfamilies. A systems approach, including Expressed Sequence Tag analysis, evolutionary analysis, protein-protein interaction network analysis and co-expression analysis, is employed to validate the clustering results, the results of which also indicates that the transcription factors from different subfamilies show uncorrelated responses.

Original languageEnglish (US)
Article numberS10
JournalBMC bioinformatics
Volume14
Issue numberSUPPL13
DOIs
StatePublished - Oct 1 2013

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Transcription factors
Fuzzy clustering
Fuzzy Clustering
Transcription Factor
Cluster Analysis
Transcription Factors
Interaction
Clustering Methods
Proteins
Gene expression regulation
Protein Interaction Maps
Arabidopsis Thaliana
Soybean
Functional Model
Domain Model
Protein Interaction Networks
Expressed Sequence Tags
Gene Expression Regulation
Network Analysis
Protein-protein Interaction

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Fuzzy clustering of CPP family in plants with evolution and interaction analyses. / Lu, Tao; Dou, Yongchao; Zhang, Chi.

In: BMC bioinformatics, Vol. 14, No. SUPPL13, S10, 01.10.2013.

Research output: Contribution to journalArticle

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