ArticlePLoS computational biology2009
Decomposition of gene expression state space trajectories.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Drug Discovery from Gene Expression/Gene Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Degree of Freedom of Gene Expression in Saccharomyces cerevisiae.Microbiology spectrum · 2022Article
- Dynamic patterns of microRNA expression during acute myeloid leukemia state-transition.Science advances · 2022Article
- Roadmap on plasticity and epigenetics in cancer.Physical biology · 2022Review
- Dual Mechanisms of Metabolism and Gene Expression of the CCRF-CEM Leukemia Cells under Glucocorticoid Treatment.International journal of molecular sciences · 2021Article
- Article
- Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks.Scientific reports · 2019Article
- Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer.Cancer research · 2018Article
- Statistical and integrative system-level analysis of DNA methylation data.Nature reviews. Genetics · 2018Review
- A roadmap towards personalized immunology.NPJ systems biology and applications · 2018Article
- Superenhancer Analysis Defines Novel Epigenomic Subtypes of Non-APL AML, Including an RARα Dependency Targetable by SY-1425, a Potent and Selective RARα Agonist.Cancer discovery · 2017Article
- Identifying time-delayed gene regulatory networks via an evolvable hierarchical recurrent neural network.BioData mining · 2017Article
- Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks.NPJ systems biology and applications · 2016Article
- Integrative analysis of cancer imaging readouts by networks.Molecular oncology · 2015Review
- Article
- Fractal dimensions of in vitro tumor cell proliferation.Journal of oncology · 2015Article
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development.PloS one · 2013Article
- Expression cartography of human tissues using self organizing maps.BMC bioinformatics · 2011Article
- Article
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2 authors.
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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.
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