Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation
The primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts fro...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-12-01
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| Series: | Frontiers in Bioengineering and Biotechnology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00062/full |
| _version_ | 1828485263887695872 |
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| author | Tunahan eCakir Mohammad Jafar Khatibipour Mohammad Jafar Khatibipour |
| author_facet | Tunahan eCakir Mohammad Jafar Khatibipour Mohammad Jafar Khatibipour |
| author_sort | Tunahan eCakir |
| collection | DOAJ |
| description | The primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts from genome-scale metabolic networks, which cover all possible reactions known to occur in the related organism in a condition-independent manner, and applies methods such as the optimization-based Flux Balance Analysis to elucidate the active network. The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization based methods to extract information content of the data such that the active network is inferred. These approaches, termed bottom-up and top-down respectively, are currently employed independently. However, considering that both approaches have the same goal, they can both benefit from each other paving the way for the novel integrative analysis methods of metabolome data- and flux- analysis approaches in the post-genomic era. This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two approaches to shed better light on how the metabolism functions. |
| first_indexed | 2024-12-11T09:09:58Z |
| format | Article |
| id | doaj.art-4bdaa68e3ad9441aa223f60226c63ca2 |
| institution | Directory Open Access Journal |
| issn | 2296-4185 |
| language | English |
| last_indexed | 2024-12-11T09:09:58Z |
| publishDate | 2014-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioengineering and Biotechnology |
| spelling | doaj.art-4bdaa68e3ad9441aa223f60226c63ca22022-12-22T01:13:31ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852014-12-01210.3389/fbioe.2014.00062120053Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliationTunahan eCakir0Mohammad Jafar Khatibipour1Mohammad Jafar Khatibipour2Gebze Institute of TechnologyGebze Institute of TechnologyGebze Institute of TechnologyThe primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts from genome-scale metabolic networks, which cover all possible reactions known to occur in the related organism in a condition-independent manner, and applies methods such as the optimization-based Flux Balance Analysis to elucidate the active network. The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization based methods to extract information content of the data such that the active network is inferred. These approaches, termed bottom-up and top-down respectively, are currently employed independently. However, considering that both approaches have the same goal, they can both benefit from each other paving the way for the novel integrative analysis methods of metabolome data- and flux- analysis approaches in the post-genomic era. This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two approaches to shed better light on how the metabolism functions.http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00062/fullMetabolomeFlux balance analysisnetwork biologyreverse engineeringconstraint-based modelsmetabolic network inference |
| spellingShingle | Tunahan eCakir Mohammad Jafar Khatibipour Mohammad Jafar Khatibipour Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation Frontiers in Bioengineering and Biotechnology Metabolome Flux balance analysis network biology reverse engineering constraint-based models metabolic network inference |
| title | Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation |
| title_full | Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation |
| title_fullStr | Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation |
| title_full_unstemmed | Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation |
| title_short | Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation |
| title_sort | metabolic network discovery by top down and bottom up approaches and paths for reconciliation |
| topic | Metabolome Flux balance analysis network biology reverse engineering constraint-based models metabolic network inference |
| url | http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00062/full |
| work_keys_str_mv | AT tunahanecakir metabolicnetworkdiscoverybytopdownandbottomupapproachesandpathsforreconciliation AT mohammadjafarkhatibipour metabolicnetworkdiscoverybytopdownandbottomupapproachesandpathsforreconciliation AT mohammadjafarkhatibipour metabolicnetworkdiscoverybytopdownandbottomupapproachesandpathsforreconciliation |