Constructing biological pathways by a two-step counting approach.

Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be charac...

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Autores principales:	Hsiuying Wang, Henry Horng-Shing Lu, Tung-Hung Chueh
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/15a6077c4ecb46dbb7d6fc4ac71d441e
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id	oai:doaj.org-article:15a6077c4ecb46dbb7d6fc4ac71d441e
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spelling	oai:doaj.org-article:15a6077c4ecb46dbb7d6fc4ac71d441e2021-11-18T06:52:45ZConstructing biological pathways by a two-step counting approach.1932-620310.1371/journal.pone.0020074https://doaj.org/article/15a6077c4ecb46dbb7d6fc4ac71d441e2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21673799/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network.Hsiuying WangHenry Horng-Shing LuTung-Hung ChuehPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 6, p e20074 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hsiuying Wang Henry Horng-Shing Lu Tung-Hung Chueh Constructing biological pathways by a two-step counting approach.
description	Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network.
format	article
author	Hsiuying Wang Henry Horng-Shing Lu Tung-Hung Chueh
author_facet	Hsiuying Wang Henry Horng-Shing Lu Tung-Hung Chueh
author_sort	Hsiuying Wang
title	Constructing biological pathways by a two-step counting approach.
title_short	Constructing biological pathways by a two-step counting approach.
title_full	Constructing biological pathways by a two-step counting approach.
title_fullStr	Constructing biological pathways by a two-step counting approach.
title_full_unstemmed	Constructing biological pathways by a two-step counting approach.
title_sort	constructing biological pathways by a two-step counting approach.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/15a6077c4ecb46dbb7d6fc4ac71d441e
work_keys_str_mv	AT hsiuyingwang constructingbiologicalpathwaysbyatwostepcountingapproach AT henryhorngshinglu constructingbiologicalpathwaysbyatwostepcountingapproach AT tunghungchueh constructingbiologicalpathwaysbyatwostepcountingapproach
_version_	1718424213301231616

Constructing biological pathways by a two-step counting approach.

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