Finding the shortest path with PesCa: a tool for network reconstruction [version 2; peer review: 2 approved, 2 approved with reservations]

Network analysis is of growing interest in several fields ranging from economics to biology. Several methods have been developed to investigate different properties of physical networks abstracted as graphs, including quantification of specific topological properties, contextual data enrichment, sim...

Full description

Saved in:
Bibliographic Details
Published inF1000 research Vol. 4; p. 484
Main Authors Scardoni, Giovanni, Tosadori, Gabriele, Pratap, Sakshi, Spoto, Fausto, Laudanna, Carlo
Format Journal Article
LanguageEnglish
Published London Faculty of 1000 Ltd 01.01.2015
F1000Research
F1000 Research Ltd
Subjects
Online AccessGet full text

Cover

Loading…
More Information
Summary:Network analysis is of growing interest in several fields ranging from economics to biology. Several methods have been developed to investigate different properties of physical networks abstracted as graphs, including quantification of specific topological properties, contextual data enrichment, simulation of pathway dynamics and visual representation. In this context, the PesCa app for the Cytoscape network analysis environment is specifically designed to help researchers infer and manipulate networks based on the shortest path principle. PesCa offers different algorithms allowing network reconstruction and analysis starting from a list of genes, proteins and in general a set of interconnected nodes. The app is useful in the early stage of network analysis, i.e. to create networks or generate clusters based on shortest path computation, but can also help further investigations and, in general, it is suitable for every situation requiring the connection of a set of nodes that apparently do not share links, such as isolated nodes in sub-networks. Overall, the plugin enhances the ability of discovering interesting and not obvious relations between high dimensional sets of interacting objects.
Bibliography:new_version
GS designed and implemented the software, GT wrote the manuscript, SP implemented the software, FS participated in the design, CL participated in the design and in the revision of the manuscript.
Competing interests: No competing interest were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.6769.2