Abstract
| Original language | English |
|---|---|
| Article number | 1350004 |
| Pages (from-to) | 1-17 |
| Number of pages | 17 |
| Journal | Journal of Bioinformatics and Computational Biology |
| Volume | 11 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - 2013 |
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Reconn : A cytoscape plug-in for exploring and visualizing reactome. / Ligtenberg, W.P.A.; Bosnacki, D.; Hilbers, P.A.J.
In: Journal of Bioinformatics and Computational Biology, Vol. 11, No. 4, 1350004, 2013, p. 1-17.Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Reconn : A cytoscape plug-in for exploring and visualizing reactome
AU - Ligtenberg, W.P.A.
AU - Bosnacki, D.
AU - Hilbers, P.A.J.
PY - 2013
Y1 - 2013
N2 - Interface and visualization tools usually provide static representations of biological pathways, which can be a severe limitation: fixed pathway boundaries are used without consensus about the elements that should be included in a particular pathway; one cannot generate new pathways or produce selective views of existing pathways. Also, the tools are not capable of integrating multiple levels that conceptually can be distinguished in biological systems.We present ReConn, an interface and visualization tool for a flexible analysis of large data at multiple biological levels. ReConn (Reactome Connector) is an open source extension to Cytoscape which allows user friendly interaction with the Reactome database. ReConn can use both predefined Reactome pathways as well as generate new pathways. A pathway can be derived by starting from any given metabolite and existing pathways can be extended by adding related reactions. The tool can also retrieve alternative routes between elements of a biological network. Such an option is potentially applicable in the design and analysis of knockout experiments. ReConn displays information about multiple levels of the system in one view. With these dynamic features ReConn addresses all of the above mentioned limitations of the interface tools.
AB - Interface and visualization tools usually provide static representations of biological pathways, which can be a severe limitation: fixed pathway boundaries are used without consensus about the elements that should be included in a particular pathway; one cannot generate new pathways or produce selective views of existing pathways. Also, the tools are not capable of integrating multiple levels that conceptually can be distinguished in biological systems.We present ReConn, an interface and visualization tool for a flexible analysis of large data at multiple biological levels. ReConn (Reactome Connector) is an open source extension to Cytoscape which allows user friendly interaction with the Reactome database. ReConn can use both predefined Reactome pathways as well as generate new pathways. A pathway can be derived by starting from any given metabolite and existing pathways can be extended by adding related reactions. The tool can also retrieve alternative routes between elements of a biological network. Such an option is potentially applicable in the design and analysis of knockout experiments. ReConn displays information about multiple levels of the system in one view. With these dynamic features ReConn addresses all of the above mentioned limitations of the interface tools.
U2 - 10.1142/S0219720013500042
DO - 10.1142/S0219720013500042
M3 - Article
C2 - 23859268
VL - 11
SP - 1
EP - 17
JO - Journal of Bioinformatics and Computational Biology
JF - Journal of Bioinformatics and Computational Biology
SN - 0219-7200
IS - 4
M1 - 1350004
ER -