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Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae

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Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. / Emmert-Streib, Frank; Dehmer, Matthias.

julkaisussa: BMC Systems Biology, Vuosikerta 3, 76, 20.07.2009.

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Emmert-Streib, Frank ; Dehmer, Matthias. / Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. Julkaisussa: BMC Systems Biology. 2009 ; Vuosikerta 3.

Bibtex - Lataa

@article{8b448949bd1340a2ab2743b9c20c61f4,
title = "Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae",
abstract = "Background: Gene networks are a representation of molecular interactions among genes or products thereof and, hence, are forming causal networks. Despite intense studies during the last years most investigations focus so far on inferential methods to reconstruct gene networks from experimental data or on their structural properties, e.g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated. Results: In the present paper we analyze cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions and not just associations or correlations between genes, and a list of known periodic genes. No further data are used. Partitioning the transcriptional regulatory network according to a graph theoretical property leads to a hierarchy in the network and, hence, in the information flow allowing to identify two groups of periodic genes. This reveals a novel conceptual interpretation of the working mechanism of the cell cycle and the genes regulated by this pathway. Conclusion: Aside from the obtained results for the cell cycle of yeast our approach could be exemplary for the analysis of general pathways by exploiting the rich causal structure of inferred and/or curated gene networks including protein or signaling networks.",
author = "Frank Emmert-Streib and Matthias Dehmer",
year = "2009",
month = "7",
day = "20",
doi = "10.1186/1752-0509-3-76",
language = "English",
volume = "3",
journal = "BMC Systems Biology",
issn = "1752-0509",
publisher = "Springer Verlag",

}

RIS (suitable for import to EndNote) - Lataa

TY - JOUR

T1 - Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae

AU - Emmert-Streib, Frank

AU - Dehmer, Matthias

PY - 2009/7/20

Y1 - 2009/7/20

N2 - Background: Gene networks are a representation of molecular interactions among genes or products thereof and, hence, are forming causal networks. Despite intense studies during the last years most investigations focus so far on inferential methods to reconstruct gene networks from experimental data or on their structural properties, e.g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated. Results: In the present paper we analyze cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions and not just associations or correlations between genes, and a list of known periodic genes. No further data are used. Partitioning the transcriptional regulatory network according to a graph theoretical property leads to a hierarchy in the network and, hence, in the information flow allowing to identify two groups of periodic genes. This reveals a novel conceptual interpretation of the working mechanism of the cell cycle and the genes regulated by this pathway. Conclusion: Aside from the obtained results for the cell cycle of yeast our approach could be exemplary for the analysis of general pathways by exploiting the rich causal structure of inferred and/or curated gene networks including protein or signaling networks.

AB - Background: Gene networks are a representation of molecular interactions among genes or products thereof and, hence, are forming causal networks. Despite intense studies during the last years most investigations focus so far on inferential methods to reconstruct gene networks from experimental data or on their structural properties, e.g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated. Results: In the present paper we analyze cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions and not just associations or correlations between genes, and a list of known periodic genes. No further data are used. Partitioning the transcriptional regulatory network according to a graph theoretical property leads to a hierarchy in the network and, hence, in the information flow allowing to identify two groups of periodic genes. This reveals a novel conceptual interpretation of the working mechanism of the cell cycle and the genes regulated by this pathway. Conclusion: Aside from the obtained results for the cell cycle of yeast our approach could be exemplary for the analysis of general pathways by exploiting the rich causal structure of inferred and/or curated gene networks including protein or signaling networks.

UR - http://www.scopus.com/inward/record.url?scp=68949220295&partnerID=8YFLogxK

U2 - 10.1186/1752-0509-3-76

DO - 10.1186/1752-0509-3-76

M3 - Article

VL - 3

JO - BMC Systems Biology

JF - BMC Systems Biology

SN - 1752-0509

M1 - 76

ER -