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Network tuned multiple rank aggregation and applications to gene ranking

With the development of various high throughput technologies and analysis methods, researchers can study different aspects of a biological phenomenon simultaneously or one aspect repeatedly with different experimental techniques and analysis methods. The output from each study is a rank list of comp...

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Detalles Bibliográficos
Autores principales: Wang, Wenhui, Zhou, Xianghong Jasmine, Liu, Zhenqiu, Sun, Fengzhu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331705/
https://www.ncbi.nlm.nih.gov/pubmed/25708095
http://dx.doi.org/10.1186/1471-2105-16-S1-S6
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author Wang, Wenhui
Zhou, Xianghong Jasmine
Liu, Zhenqiu
Sun, Fengzhu
author_facet Wang, Wenhui
Zhou, Xianghong Jasmine
Liu, Zhenqiu
Sun, Fengzhu
author_sort Wang, Wenhui
collection PubMed
description With the development of various high throughput technologies and analysis methods, researchers can study different aspects of a biological phenomenon simultaneously or one aspect repeatedly with different experimental techniques and analysis methods. The output from each study is a rank list of components of interest. Aggregation of the rank lists of components, such as proteins, genes and single nucleotide variants (SNV), produced by these experiments has been proven to be helpful in both filtering the noise and bringing forth a more complete understanding of the biological problems. Current available rank aggregation methods do not consider the network information that has been observed to provide vital contributions in many data integration studies. We developed network tuned rank aggregation methods incorporating network information and demonstrated its superior performance over aggregation methods without network information. The methods are tested on predicting the Gene Ontology function of yeast proteins. We validate the methods using combinations of three gene expression data sets and three protein interaction networks as well as an integrated network by combining the three networks. Results show that the aggregated rank lists are more meaningful if protein interaction network is incorporated. Among the methods compared, CGI_RRA and CGI_Endeavour, which integrate rank lists with networks using CGI [1] followed by rank aggregation using either robust rank aggregation (RRA) [2] or Endeavour [3] perform the best. Finally, we use the methods to locate target genes of transcription factors.
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spelling pubmed-43317052015-03-19 Network tuned multiple rank aggregation and applications to gene ranking Wang, Wenhui Zhou, Xianghong Jasmine Liu, Zhenqiu Sun, Fengzhu BMC Bioinformatics Proceedings With the development of various high throughput technologies and analysis methods, researchers can study different aspects of a biological phenomenon simultaneously or one aspect repeatedly with different experimental techniques and analysis methods. The output from each study is a rank list of components of interest. Aggregation of the rank lists of components, such as proteins, genes and single nucleotide variants (SNV), produced by these experiments has been proven to be helpful in both filtering the noise and bringing forth a more complete understanding of the biological problems. Current available rank aggregation methods do not consider the network information that has been observed to provide vital contributions in many data integration studies. We developed network tuned rank aggregation methods incorporating network information and demonstrated its superior performance over aggregation methods without network information. The methods are tested on predicting the Gene Ontology function of yeast proteins. We validate the methods using combinations of three gene expression data sets and three protein interaction networks as well as an integrated network by combining the three networks. Results show that the aggregated rank lists are more meaningful if protein interaction network is incorporated. Among the methods compared, CGI_RRA and CGI_Endeavour, which integrate rank lists with networks using CGI [1] followed by rank aggregation using either robust rank aggregation (RRA) [2] or Endeavour [3] perform the best. Finally, we use the methods to locate target genes of transcription factors. BioMed Central 2015-01-21 /pmc/articles/PMC4331705/ /pubmed/25708095 http://dx.doi.org/10.1186/1471-2105-16-S1-S6 Text en Copyright © 2015 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Wang, Wenhui
Zhou, Xianghong Jasmine
Liu, Zhenqiu
Sun, Fengzhu
Network tuned multiple rank aggregation and applications to gene ranking
title Network tuned multiple rank aggregation and applications to gene ranking
title_full Network tuned multiple rank aggregation and applications to gene ranking
title_fullStr Network tuned multiple rank aggregation and applications to gene ranking
title_full_unstemmed Network tuned multiple rank aggregation and applications to gene ranking
title_short Network tuned multiple rank aggregation and applications to gene ranking
title_sort network tuned multiple rank aggregation and applications to gene ranking
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331705/
https://www.ncbi.nlm.nih.gov/pubmed/25708095
http://dx.doi.org/10.1186/1471-2105-16-S1-S6
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