title: Fuzzy clustering of CPP family in plants with evolution and interaction analyses.
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.
  
  
  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.
authors.forename: Tao
authors.initials: T
authors.lastname: Lu
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Dou
authors.forename: Chi
authors.initials: C
authors.lastname: Zhang
mesh_terms: D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D003545:Cysteine / Q000235:genetics*; D017143:Fuzzy Logic; D020869:Gene Expression Profiling; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D025941:Protein Interaction Mapping; D014157:Transcription Factors
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins; D014157:Transcription Factors; D003545:Cysteine