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This article is part of the supplement: Selected articles from the 9th Annual Biotechnology and Bioinformatics Symposium (BIOT 2012)

Open Access Research

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

Tao Lu, Yongchao Dou and Chi Zhang*

Author Affiliations

School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA

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BMC Bioinformatics 2013, 14(Suppl 13):S10  doi:10.1186/1471-2105-14-S13-S10

Published: 1 October 2013

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.