Decomposition of gene expression state space trajectories.

Representing and analyzing complex networks remains a roadblock to creating dynamic network models of biological processes and pathways. The study of cell fate transitions can reveal much about the transcriptional regulatory programs that underlie these phenotypic changes and give rise to the coordi...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jessica C Mar, John Quackenbush
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/cd35d5efcdfe4e87b8d4ad411e3fdee2
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:cd35d5efcdfe4e87b8d4ad411e3fdee2
record_format	dspace
spelling	oai:doaj.org-article:cd35d5efcdfe4e87b8d4ad411e3fdee22021-11-25T05:42:44ZDecomposition of gene expression state space trajectories.1553-734X1553-735810.1371/journal.pcbi.1000626https://doaj.org/article/cd35d5efcdfe4e87b8d4ad411e3fdee22009-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20041215/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Representing and analyzing complex networks remains a roadblock to creating dynamic network models of biological processes and pathways. The study of cell fate transitions can reveal much about the transcriptional regulatory programs that underlie these phenotypic changes and give rise to the coordinated patterns in expression changes that we observe. The application of gene expression state space trajectories to capture cell fate transitions at the genome-wide level is one approach currently used in the literature. In this paper, we analyze the gene expression dataset of Huang et al. (2005) which follows the differentiation of promyelocytes into neutrophil-like cells in the presence of inducers dimethyl sulfoxide and all-trans retinoic acid. Huang et al. (2005) build on the work of Kauffman (2004) who raised the attractor hypothesis, stating that cells exist in an expression landscape and their expression trajectories converge towards attractive sites in this landscape. We propose an alternative interpretation that explains this convergent behavior by recognizing that there are two types of processes participating in these cell fate transitions-core processes that include the specific differentiation pathways of promyelocytes to neutrophils, and transient processes that capture those pathways and responses specific to the inducer. Using functional enrichment analyses, specific biological examples and an analysis of the trajectories and their core and transient components we provide a validation of our hypothesis using the Huang et al. (2005) dataset.Jessica C MarJohn QuackenbushPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 12, p e1000626 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jessica C Mar John Quackenbush Decomposition of gene expression state space trajectories.
description	Representing and analyzing complex networks remains a roadblock to creating dynamic network models of biological processes and pathways. The study of cell fate transitions can reveal much about the transcriptional regulatory programs that underlie these phenotypic changes and give rise to the coordinated patterns in expression changes that we observe. The application of gene expression state space trajectories to capture cell fate transitions at the genome-wide level is one approach currently used in the literature. In this paper, we analyze the gene expression dataset of Huang et al. (2005) which follows the differentiation of promyelocytes into neutrophil-like cells in the presence of inducers dimethyl sulfoxide and all-trans retinoic acid. Huang et al. (2005) build on the work of Kauffman (2004) who raised the attractor hypothesis, stating that cells exist in an expression landscape and their expression trajectories converge towards attractive sites in this landscape. We propose an alternative interpretation that explains this convergent behavior by recognizing that there are two types of processes participating in these cell fate transitions-core processes that include the specific differentiation pathways of promyelocytes to neutrophils, and transient processes that capture those pathways and responses specific to the inducer. Using functional enrichment analyses, specific biological examples and an analysis of the trajectories and their core and transient components we provide a validation of our hypothesis using the Huang et al. (2005) dataset.
format	article
author	Jessica C Mar John Quackenbush
author_facet	Jessica C Mar John Quackenbush
author_sort	Jessica C Mar
title	Decomposition of gene expression state space trajectories.
title_short	Decomposition of gene expression state space trajectories.
title_full	Decomposition of gene expression state space trajectories.
title_fullStr	Decomposition of gene expression state space trajectories.
title_full_unstemmed	Decomposition of gene expression state space trajectories.
title_sort	decomposition of gene expression state space trajectories.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/cd35d5efcdfe4e87b8d4ad411e3fdee2
work_keys_str_mv	AT jessicacmar decompositionofgeneexpressionstatespacetrajectories AT johnquackenbush decompositionofgeneexpressionstatespacetrajectories
_version_	1718414485941649408

Decomposition of gene expression state space trajectories.

Ejemplares similares