Bottleneck genes and community structure in the cell cycle network of S. pombe.
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 wh...
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2007-06-01
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Series: | PLoS Computational Biology |
Online Access: | https://doi.org/10.1371/journal.pcbi.0030103 |
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doaj-3f00d04e67ef4c5da841fffde4e4e7dd2021-04-21T15:08:57ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582007-06-0136e10310.1371/journal.pcbi.0030103Bottleneck genes and community structure in the cell cycle network of S. pombe.Cécile Caretta-CartozoPaolo De Los RiosFrancesco PiazzaPietro LiòThe 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.https://doi.org/10.1371/journal.pcbi.0030103 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cécile Caretta-Cartozo Paolo De Los Rios Francesco Piazza Pietro Liò |
spellingShingle |
Cécile Caretta-Cartozo Paolo De Los Rios Francesco Piazza Pietro Liò Bottleneck genes and community structure in the cell cycle network of S. pombe. PLoS Computational Biology |
author_facet |
Cécile Caretta-Cartozo Paolo De Los Rios Francesco Piazza Pietro Liò |
author_sort |
Cécile Caretta-Cartozo |
title |
Bottleneck genes and community structure in the cell cycle network of S. pombe. |
title_short |
Bottleneck genes and community structure in the cell cycle network of S. pombe. |
title_full |
Bottleneck genes and community structure in the cell cycle network of S. pombe. |
title_fullStr |
Bottleneck genes and community structure in the cell cycle network of S. pombe. |
title_full_unstemmed |
Bottleneck genes and community structure in the cell cycle network of S. pombe. |
title_sort |
bottleneck genes and community structure in the cell cycle network of s. pombe. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2007-06-01 |
description |
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. |
url |
https://doi.org/10.1371/journal.pcbi.0030103 |
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