dorsal/arxiv
View SchemaFunctionality Encoded In Topology? Discovering Macroscopic Regulatory Modules from Large-Scale Protein-DNA Interaction Networks
| Authors | Riccardo Boscolo, Behnam A. Rezaei, P. Oscar Boykin, Vwani P. Roychowdhury |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0501039 |
| URL | https://arxiv.org/abs/q-bio/0501039 |
Abstract
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in other biological problems (e.g. DNA sequencing) will be as effective when it comes to inferring more complex intracellular processes. The results in this paper address this fundamental issue in the specific context of transcription regulatory networks. Although simple recurring regulatory motifs have been identified in the past, due to the size and complexity of the connectivity structure, the subdivision of such networks into larger, and possibly inter-connected, regulatory modules is still under investigation. Specifically, it is unclear whether functionally well-characterized transcriptional sub-networks can be identified by solely analyzing the connectivity structure of the overall network topology. In this paper, we show that transcriptional regulatory networks can be systematically partitioned into communities whose members are consistently functionally related. We applied the partitioning method to the transcriptional regulatory networks of the yeast Saccharomyces cerevisiae; the resulting communities of gene and transcriptional regulators can be associated to distinct functional units, such as amino acid metabolism, cell cycle regulation, protein biosynthesis and localization, DNA replication and maintenance, lipid catabolism, stress response and so on. Moreover, the observation of inter-community connectivity patterns provides a valuable tool for elucidating the inter-dependency between the discovered regulatory modules.
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"abstract": "The promise of discovering a functional blueprint of a cellular system from\nlarge-scale and high-throughput sequence and experimental data is predicated on\nthe belief that the same top-down investigative approach that proved successful\nin other biological problems (e.g. DNA sequencing) will be as effective when it\ncomes to inferring more complex intracellular processes. The results in this\npaper address this fundamental issue in the specific context of transcription\nregulatory networks. Although simple recurring regulatory motifs have been\nidentified in the past, due to the size and complexity of the connectivity\nstructure, the subdivision of such networks into larger, and possibly\ninter-connected, regulatory modules is still under investigation. Specifically,\nit is unclear whether functionally well-characterized transcriptional\nsub-networks can be identified by solely analyzing the connectivity structure\nof the overall network topology. In this paper, we show that transcriptional\nregulatory networks can be systematically partitioned into communities whose\nmembers are consistently functionally related. We applied the partitioning\nmethod to the transcriptional regulatory networks of the yeast Saccharomyces\ncerevisiae; the resulting communities of gene and transcriptional regulators\ncan be associated to distinct functional units, such as amino acid metabolism,\ncell cycle regulation, protein biosynthesis and localization, DNA replication\nand maintenance, lipid catabolism, stress response and so on. Moreover, the\nobservation of inter-community connectivity patterns provides a valuable tool\nfor elucidating the inter-dependency between the discovered regulatory modules.",
"arxiv_id": "q-bio/0501039",
"authors": [
"Riccardo Boscolo",
"Behnam A. Rezaei",
"P. Oscar Boykin",
"Vwani P. Roychowdhury"
],
"categories": [
"q-bio.MN",
"cond-mat.dis-nn"
],
"title": "Functionality Encoded In Topology? Discovering Macroscopic Regulatory Modules from Large-Scale Protein-DNA Interaction Networks",
"url": "https://arxiv.org/abs/q-bio/0501039"
},
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