PathwayMatcher v1.8

PathwayMatcher v1.8

Free, open-source command line program to search for reactions and pathways related to input data.

Project structure:

• PathwayMatcher: Main program to load the static mapping and call other methods. Contains no implementation of the search or analysis methods, just as dependencies.
• Model: Classes to represent the objects related to pathway analysis.
• Methods: Separate jar with the search and analysis methods. They are called with the static mapping sent as arguments.
• Extractor: Predecesor project executed localy. Creates static mapping files. Not shipped with PathwayMatcher.

Performs:

• Pathway search in Reactome
• Over representation analysis
• Exports connection graph

Shipped as:

• Self contained executable Jar file
• Docker image

What is included in the package:

• The PathwayMatcher program
• Mapping files for all supported data types

Requirements to run:

• Java 1.8+
• Neo4j with Reactome only for extractor, not for pathway matcher.

Pathway data sources:

• Reactome graph database v63.
• Variant effect predictors (VEP) mapping

Input

The input data types supported are:

• Gene names
• Ensembl identifiers
• UniProt accessions
• Rsid genetic variants
• Genetic variants specified by chromosome and base pair
• Proteoforms

Output

• Search: Tab separated file with the list of reactions and pathways related to each input entity
• Analysis: Tab separated file with the list of most statistically significant pathways
• Igraph: Two tab separated files for vertices and edges.

Proteoforms

• Each proteoform is formed by a uniprot accession number + the isoform + the set of post translational modifications.
• Each post translational modification is composed by a PSIMOD type and a positive integer coordinate.

Command line arguments accepted are:

• t, type
• r, range
• tlp, toplevelpathways
• m, matching : (new) Superset, subset, One and Strict
• i, input
• o, output
• g, graph
• (new) f, fast

New features:

• PathwayMatcher considers only proper chemical reactions in Reactome, ignoring the Blackbox events and others uncertain processes.
• The Peptide input types need an argument for the fasta file.