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KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions

KUPS (The University of Kansas Proteomics Service) provides high-quality protein–protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interactin...

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Detalles Bibliográficos
Autores principales: Chen, Xue-wen, Jeong, Jong Cheol, Dermyer, Patrick
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013794/
https://www.ncbi.nlm.nih.gov/pubmed/20952400
http://dx.doi.org/10.1093/nar/gkq943
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author Chen, Xue-wen
Jeong, Jong Cheol
Dermyer, Patrick
author_facet Chen, Xue-wen
Jeong, Jong Cheol
Dermyer, Patrick
author_sort Chen, Xue-wen
collection PubMed
description KUPS (The University of Kansas Proteomics Service) provides high-quality protein–protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, which includes 185 446 IPPs and ∼1.5 billion NIPs from five primary databases: IntAct, HPRD, MINT, UniProt and the Gene Ontology. The IPP set can be set to specific model organisms, interaction types and experimental evidence. The NIP set can be generated using four different strategies, which can alleviate biased estimation problems. Lastly, multiple features can be provided for all of the IPP and NIP pairs. Additionally, KUPS provides two benchmark data sets to help researchers compare their algorithms to existing approaches. KUPS is freely available at http://www.ittc.ku.edu/chenlab.
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spelling pubmed-30137942011-01-03 KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions Chen, Xue-wen Jeong, Jong Cheol Dermyer, Patrick Nucleic Acids Res Articles KUPS (The University of Kansas Proteomics Service) provides high-quality protein–protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, which includes 185 446 IPPs and ∼1.5 billion NIPs from five primary databases: IntAct, HPRD, MINT, UniProt and the Gene Ontology. The IPP set can be set to specific model organisms, interaction types and experimental evidence. The NIP set can be generated using four different strategies, which can alleviate biased estimation problems. Lastly, multiple features can be provided for all of the IPP and NIP pairs. Additionally, KUPS provides two benchmark data sets to help researchers compare their algorithms to existing approaches. KUPS is freely available at http://www.ittc.ku.edu/chenlab. Oxford University Press 2011-01 2010-10-15 /pmc/articles/PMC3013794/ /pubmed/20952400 http://dx.doi.org/10.1093/nar/gkq943 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Chen, Xue-wen
Jeong, Jong Cheol
Dermyer, Patrick
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
title KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
title_full KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
title_fullStr KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
title_full_unstemmed KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
title_short KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
title_sort kups: constructing datasets of interacting and non-interacting protein pairs with associated attributions
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013794/
https://www.ncbi.nlm.nih.gov/pubmed/20952400
http://dx.doi.org/10.1093/nar/gkq943
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