ArticlePLoS computational biology2007
Bottleneck genes and community structure in the cell cycle network of S. pombe.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast.BMC genomics · 2009Pooled it
- A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data.Frontiers in genetics · 2018Article
- Comparative analysis of a novel disease phenotype network based on clinical manifestations.Journal of biomedical informatics · 2015Article
- Article
- Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species.Nucleic acids research · 2012Article
- Determining modular organization of protein interaction networks by maximizing modularity density.BMC systems biology · 2010Article
- Characterizing regulatory path motifs in integrated networks using perturbational data.Genome biology · 2010Article
- Clinical bioinformatics for complex disorders: a schizophrenia case study.BMC bioinformatics · 2009Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of cell cycle-related genes is still a difficult task, even for organisms with relatively few genes such as the fission yeast. Several gene expression studies have been published on S. pombe showing similarities but also discrepancies in their results. We introduce a network in which the weight of each link is a function of the phase difference between the expression peaks of two genes. The analysis of the stability of the clustering through the computation of an entropy parameter reveals a structure made of four clusters, the first one corresponding to a robustly connected M-G1 component, the second to genes in the S phase, and the third and fourth to two G2 components. They are separated by bottleneck structures that appear to correspond to cell cycle checkpoints. We identify a number of genes that are located on these bottlenecks. They represent a novel group of cell cycle regulatory genes. They all show interesting functions, and they are supposed to be involved in the regulation of the transition from one phase to the next. We therefore present a comparison of the available studies on the fission yeast cell cycle and a general statistical bioinformatics methodology to find bottlenecks and gene community structures based on recent developments in network theory.
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