Bioinformatics and Functional Genomics Research Group
Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL)
Javier DE LAS RIVAS and Conrad DROSTE
Path2enet: generation of human pathway-derived networks in an expression specific context
Background: Biological pathways are subsets of the complex biomolecular wiring that occur in living cells.
They are usually rationalized and depicted in cartoon maps or charts to show them in a friendly visible way.
Despite these efforts to present biological pathways, the current progress of bioinformatics indicates that translation
of pathways in networks can be a very useful approach to achieve a computer-based view of the complex processes and
interactions that occurr in a living system.
Results: We have developed a bioinformatic tool called Path2enet that provides a translation of biological
pathways in protein networks integrating several layers of information about the biomolecular nodes in a multiplex view.
Path2enet is an R package that reads the relations and links between proteins stored in a comprehensive database of
biological pathways, KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/), and integrates
them with expression data from various resources and with data on protein-protein physical interactions.
Path2enet tool uses the expression data to determine if a given protein in a network (i.e., a node) is active
(ON) or inactive (OFF) in a specific cellular context or sample type. In this way, Path2enet reduces the complexity
of the networks and reveals the proteins that are active (expressed) under specific conditions. As a proof of concept,
this work presents a practical “case of use” generating the pathway-expression-networks corresponding to
the NOTCH Signaling Pathway in human B- and T-lymphocytes. This case is produced by the analysis and integration in
Path2enet of an experimental dataset of genome-wide expression microarrays produced with these cell types (i.e., B cells and T cells).
Conclusions: Path2enet is an open source and open access tool that allows the construction of pathway-expression-networks,
reading and integrating the information from biological pathways, protein interactions and gene expression cell specific data.
The development of this type of tools aims to provide a more integrative and global view of the links and associations that
exist between the proteins working in specific cellular systems.
Additional File 1: Path2enet R vignette in HTML format: Path2enet.html
Additional File 2: Path2enet R package: Path2enet_0.9.99.tar.gz
Additional File 3: Path2enet "SQL dump file" to create a MySQL database with all human pathways: Path2enet_KeggSQL.sql.zip
[ARTICLE published in BMC Genomics 2016]