TY - JOUR
T1 - Fuzzy clustering of CPP family in plants with evolution and interaction analyses
AU - Lu, Tao
AU - Dou, Yongchao
AU - Zhang, Chi
N1 - Funding Information:
The work is supported by funding under CZ’s startup funds from University of Nebraska, Lincoln, NE. This article has been published as part of BMC Bioinformatics Volume 14 Supplement 13, 2013: Selected articles from the 9th Annual Biotechnology and Bioinformatics Symposium (BIOT 2012). The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcbioinformatics/supplements/14/S13
PY - 2013/10/1
Y1 - 2013/10/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84886834757&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84886834757&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-14-S13-S10
DO - 10.1186/1471-2105-14-S13-S10
M3 - Article
C2 - 24268301
AN - SCOPUS:84886834757
VL - 14
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
IS - SUPPL13
M1 - S10
ER -