metexplore / container-pathwayenrichment

PathwayEnrichement

Version: 1.0.1

Short description

Predicts pathway enrichment in human metabolic bionetwork (Recon 2v3) from a dataset of pre-selected metabolites

Description

Metabolites extracted from the input file are mapped on a Recon network ([1]) by providing either INCHI or CHEBI information. Pathway enrichment is calculated with an exact Fisher one-tailed test and a correction test. Two files are provided in output:

• a first one containing for each metabolites from the input file: the success or the failure of the mapping (true/false), their names, those of one or several elements of the network in mapping case.
• a second one containing for each pathway containing the mapped metabolites: their names, the Fisher's P value, the Bonferroni (or other test correction) value, the list of mapped metabolites, the number of mapped metabolites and the coverage of mapped metabolites on the total of metabolites contained by the studied pathway.

Key features

• Metabolic network
• Modeling
• Pathway analysis
• Prediction

Functionality

• Post-processing
• Statistical Analysis

Tool Authors

• MetExplore Group [email protected]

Container Contributors

• Etienne Camenen (INRA Toulouse)

Git Repository

• https://github.com/phnmnl/container-pathwayEnrichment.git

Installation

For local installation of the container:

docker pull docker-registry.phenomenal-h2020.eu/phnmnl/pathwayenrichment

Usage Instructions

For direct usage of the docker image:

docker run docker-registry.phenomenal-h2020.eu/phnmnl/pathwayenrichment -i  <input file> [-o1 <output file 1>] [-o2 <output file 2>] [-s <sbml file>] [-chebi <CHEBI column>] [-inchi <InChI column>]  [-f <filtered column>] [-l <layer selection>] [-h]

• -i, -o1, -o2 and -s could be used to customize file's name respectively for the input file, the output file resulting from mapping (default: "mapping.tsv"), the one resulting from pathway enrichment (default: "pathwayEnrichment.tsv") and the sbml file where the bionetwork is extracted (default: those corresponding to Recon 2v3). Only -i is required.
• -chebi, -inchi and -foptions set column number where CHEBI, InChI and discriminant information are among the input file. With -f option, lines containing empty values among the selected column are discarded from the analysis (for example : after a statistical pre-selection). By default, they are set respectively to 2, 5 and 0 ("1" is considered as the first column). 0 or negative values are used to disable an option if the corresponding information is missing. -chebi and -inchi options could not be both disabled.
• -l selects the InChI's layers used for mapping among: connections, hydrogens atoms, charge, protons, double-bond stereo, tetrahedral sp3 stereo, isotopic atoms, fixed hydrogens and reconnected layers. These layers must be set as a list of characters containing the number separated by commas. By default, this option is set on c,h for a mapping only on connections and hydrogens atom layers. A whole layers selected must be c,h,q,p,b,t,i,f,r. For mapping on formula only, select -l option with no parameters after.
• -h option prints a help.

References

• Thiele I, Swainston N, Fleming RMT, et al. A community-driven global reconstruction of human metabolism. Nature biotechnology. 2013;31(5):10.1038/nbt.2488. doi:10.1038/nbt.2488.