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

BMC Bioinformatics

Research

Chi Zhang¹  Tao Lu¹  Yongchao Dou¹ 

[1] School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, USA;

关键词: Fuzzy Cluster;    Fuzzy Cluster Method;    Unique ESTs;    dbEST Database;    Redundant ESTs;   

DOI  :  10.1186/1471-2105-14-S13-S10

来源: Springer

【 摘 要 】

BackgroundTranscription 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.MethodsIn 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 conclusionsWith 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.

【 授权许可】

Unknown   
© Lu et al; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.