CytoSVM: an advanced server for identification of cytokine-receptor interactions

The interactions between cytokines and their complementary receptors are the gateways to properly understand a large variety of cytokine-specific cellular activities such as immunological responses and cell differentiation. To discover novel cytokine-receptor interactions, an advanced support vector...

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Main Authors:	Xu, Jin-Rui, Zhang, Jing-Xian, Han, Bu-Cong, Liang, Liang, Ji, Zhi-Liang
Format:	Online
Language:	English
Published:	Oxford University Press 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933174/

id	pubmed-1933174
recordtype	oai_dc
spelling	pubmed-19331742007-07-31 CytoSVM: an advanced server for identification of cytokine-receptor interactions Xu, Jin-Rui Zhang, Jing-Xian Han, Bu-Cong Liang, Liang Ji, Zhi-Liang Articles The interactions between cytokines and their complementary receptors are the gateways to properly understand a large variety of cytokine-specific cellular activities such as immunological responses and cell differentiation. To discover novel cytokine-receptor interactions, an advanced support vector machines (SVMs) model, CytoSVM, was constructed in this study. This model was iteratively trained using 449 mammal (except rat) cytokine-receptor interactions and about 1 million virtually generated positive and negative vectors in an enriched way. Final independent evaluation by rat's data received sensitivity of 97.4%, specificity of 99.2% and the Matthews correlation coefficient (MCC) of 0.89. This performance is better than normal SVM-based models. Upon this well-optimized model, a web-based server was created to accept primary protein sequence and present its probabilities to interact with one or several cytokines. Moreover, this model was applied to identify putative cytokine-receptor pairs in the whole genomes of human and mouse. Excluding currently known cytokine-receptor interactions, total 1609 novel cytokine-receptor pairs were discovered from human genome with probability ∼80% after further transmembrane analysis. These cover 220 novel receptors (excluding their isoforms) for 126 human cytokines. The screening results have been deposited in a database. Both the server and the database can be freely accessed at http://bioinf.xmu.edu.cn/software/cytosvm/cytosvm.php. Oxford University Press 2007-07 2007-05-25 /pmc/articles/PMC1933174/ /pubmed/17526528 http://dx.doi.org/10.1093/nar/gkm254 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Xu, Jin-Rui Zhang, Jing-Xian Han, Bu-Cong Liang, Liang Ji, Zhi-Liang
spellingShingle	Xu, Jin-Rui Zhang, Jing-Xian Han, Bu-Cong Liang, Liang Ji, Zhi-Liang CytoSVM: an advanced server for identification of cytokine-receptor interactions
author_facet	Xu, Jin-Rui Zhang, Jing-Xian Han, Bu-Cong Liang, Liang Ji, Zhi-Liang
author_sort	Xu, Jin-Rui
title	CytoSVM: an advanced server for identification of cytokine-receptor interactions
title_short	CytoSVM: an advanced server for identification of cytokine-receptor interactions
title_full	CytoSVM: an advanced server for identification of cytokine-receptor interactions
title_fullStr	CytoSVM: an advanced server for identification of cytokine-receptor interactions
title_full_unstemmed	CytoSVM: an advanced server for identification of cytokine-receptor interactions
title_sort	cytosvm: an advanced server for identification of cytokine-receptor interactions
description	The interactions between cytokines and their complementary receptors are the gateways to properly understand a large variety of cytokine-specific cellular activities such as immunological responses and cell differentiation. To discover novel cytokine-receptor interactions, an advanced support vector machines (SVMs) model, CytoSVM, was constructed in this study. This model was iteratively trained using 449 mammal (except rat) cytokine-receptor interactions and about 1 million virtually generated positive and negative vectors in an enriched way. Final independent evaluation by rat's data received sensitivity of 97.4%, specificity of 99.2% and the Matthews correlation coefficient (MCC) of 0.89. This performance is better than normal SVM-based models. Upon this well-optimized model, a web-based server was created to accept primary protein sequence and present its probabilities to interact with one or several cytokines. Moreover, this model was applied to identify putative cytokine-receptor pairs in the whole genomes of human and mouse. Excluding currently known cytokine-receptor interactions, total 1609 novel cytokine-receptor pairs were discovered from human genome with probability ∼80% after further transmembrane analysis. These cover 220 novel receptors (excluding their isoforms) for 126 human cytokines. The screening results have been deposited in a database. Both the server and the database can be freely accessed at http://bioinf.xmu.edu.cn/software/cytosvm/cytosvm.php.
publisher	Oxford University Press
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933174/
_version_	1611398574595112960

CytoSVM: an advanced server for identification of cytokine-receptor interactions

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