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Title

Insilico identification of protein-protein interactions in Silkworm, Bombyx mori

 

Authors

Ramasamy Sumathy1, 3, Ashwath Southekal Krishna Rao1, Nalavadi Chandrakanth2 & Velliyur Kanniappan Gopalakrishnan3*

 

Affiliation

1Bioinformatics centre, 2Molecular biology Laboratory, Central Sericultural Research and Training Institute, Mysore, Karnataka, India; 3Department of Biochemistry and Bioinformatics, Karpagam University, Coimbatore-641 021, Tamilnadu, India

 

Email

vkgopalakrishnan@gmail.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received January 14, 2014; Accepted January 25, 2014; Published February 19, 2014

 

Abstract

The Domesticated silkworm, Bombyx mori, an economically important insect has been used as a lepidopteran molecular model next only to Drosophila. Compared to the genomic information in silkworm, the protein-protein interaction data are limited. Therefore experimentally identified PPI maps from five model organisms such as E.coli, C.elegans, D.melanogaster, H. sapiens, S. cerevisiae were used to infer the PPI network of silkworm using the well-recognized Interlog based method. Among the 14623 silkworm proteins, 7736 protein-protein interaction pairs were predicted which include 2700 unique proteins of the silkworms. Using the iPfam interaction domains and the gene expression data, these predictions were validated. In that 625 PPI pairs of predicted network were associated with the iPfam domain-domain interactions and the random network has average of 9. In the gene expression method, the average PCC value of the predicted network and random network was 0.29 and 0.231000.00042 respectively. It reveals that the predicted PPI networks of silkworm are highly significant and reliable. This is the first PPI network for the silkworm which will provide a framework for deciphering the cellular processes governing key metabolic pathways in the silkworm, Bombyx mori and available at SilkPPI (http://210.212.197.30/SilkPPI/). 

 

Keywords

protein-protein interaction, Interlog method, Bombyx mori

 

Citation

Sumathy et al.   Bioinformation 10(2): 056-062 (2014)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.