Network Biomass WormPaths

FBAFlux Balance Analysis PEAPathway Enrichment Analysis

WormClustClustering- and enrichment-based association of genes with the metabolic network

Walhout Lab web page:
walhoutlab.umassmed.edu

Email for WormFlux:
lutfu.yilmaz@umassmed.edu

Metabolic Network Model

You can download the current metabolic network model in the following formats:

	Link to file
SBML (?) Systems Biology Markup Language, Level 3, Version 1	iCEL1314.xml
JSON (?) JavaScript Object Notation format	iCEL1314.json
MS Excel (?) Spreadsheet created in Microsoft Excel	iCEL1314.xlsx
mat (?) MATLAB structure for use with COBRA toolbox.	iCEL1314.mat

WormPaths and Pathway Enrichment Analysis (PEA)

The following files cover gene annotations in WormPaths and PEA:

	Link to file
Categorized genes (?) List of WormBase IDs and gene names for model genes that are assigned to pathways or categories.	iCELgenes.csv
Pathways and categories (?) Pathways or categories for gene annotation at four levels of resolution.	CategoriesAtFourLevels.tsv
Gene sets (?) Sets of genes assigned to each pathway or category at the four levels of annotation.	GeneSetsAtFourLevels_WBID.xls

pan-iCEL Model (?) An expanding network that covers metabolites detected and reactions annotated in not just N2, which is the strain the iCEL model is based on, but also other strains being studied. See Fox et al., 2022 (PMID: 35794472) for details.

We also have an extended network model that harbors reactions annotated in multiple C. elegans strains (Fox et al., 2022):

	Link to file
SBML (?) Systems Biology Markup Language, Level 3, Version 1	pan-iCEL v1.0.xml
JSON (?) JavaScript Object Notation format	pan-iCEL v1.0.json
mat (?) MATLAB structure for use with COBRA toolbox.	pan-iCEL v1.0.mat

The information and tools provided in this website are to be used for academic purposes only.