![]() The development of those pathway repositories has also fueled the creation of standard representations and formats, to facilitate the exchange and representation of data, such as the Biological Pathway Exchange standard (BioPAX), the Systems Biology Markup Language (SBML) or the Systems Biology Graphical Notation (SBGN). For example, it is now a very common practice to cross the output of high-throughput experiments, such as mRNA or protein expression levels, with curated biological pathways in order to visualize changes, analyze their impact on a network and formulate new hypotheses about biological processes. All these pathway and biological network databases facilitate a large spectrum of analyses, improving our understanding of cellular systems. A large body of knowledge on cellular biochemistry is organized in publicly available repositories such as the KEGG database, Reactome, MINT, or the Cancer Cell Map ( ). At last, we illustrate some of the BiNoM functions on a detailed biological case study of a network representing the G1/S transition of the cell cycle, a crucial cellular process disturbed in most human tumors.īiological pathways and networks comprise sets of interactions, or functional relationships, occurring at the molecular level in living cells. Here, we provide an in-depth overview of the BiNoM functions, and we also detail novel aspects such as the support of the BioPAX Level 3 format and the implementation of a new algorithm for the quantification of pathways for influence networks. BiNoM also implements a collection of powerful graph-based functions and algorithms such as path analysis, decomposition by involvement of an entity or cyclic decomposition, subnetworks clustering and decomposition of a large network in modules. As such, BiNoM is able to efficiently manage large BioPAX files such as whole pathway databases (e.g. BiNoM provides a set of functions allowing to import BioPAX files, but also to search and edit their content. BiNoM can be used to import and analyze files created with the CellDesigner software. We have developed BiNoM (Biological Network Manager), a Cytoscape plugin, which provides functions for the import-export of some standard systems biology file formats (import from CellDesigner, BioPAX Level 3 and CSML export to SBML, CellDesigner and BioPAX Level 3), and a set of algorithms to analyze and reduce the complexity of biological networks. However, large-scale molecular maps are not always easy to mine and interpret. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the formulation of new biological hypotheses to be tested, a fundamental principle of the systems biology approach. Public repositories of biological pathways and networks have greatly expanded in recent years.
0 Comments
Leave a Reply. |