Decomposition of Gene Expression State Space Trajectories

DSpace/Manakin Repository

Decomposition of Gene Expression State Space Trajectories

Citable link to this page

 

 
Title: Decomposition of Gene Expression State Space Trajectories
Author: Mar, Jessica Cara; Quackenbush, John

Note: Order does not necessarily reflect citation order of authors.

Citation: Mar, Jessica C., and John Quackenbush. 2009. Decomposition of Gene Expression State Space Trajectories. PLoS Computational Biology 5(12).
Full Text & Related Files:
Abstract: 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.
Published Version: doi:10.1371/journal.pcbi.1000626
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791157/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4553228
Downloads of this work:

Show full Dublin Core record

This item appears in the following Collection(s)

 
 

Search DASH


Advanced Search
 
 

Submitters