Combined metabolic and signaling interaction network (MetaPKN)
==============================================================

Update 27 May 2021
------------------

The Meta PKN has been replaced by a new, streamlined method
working from the redHuman reaction network. The new version
is available in this directory (cosmos_PKN) and from here:
https://github.com/saezlab/cosmos_meta_PKN_redhuman 

The old Meta PKN is archived here for reproducibility
purposes.

Meta PKN
--------

This directory contains combined signaling and metabolic network
data constructed by using the Recon3D and STITCH metabolic
networks and the signaling network of OmniPath.

The scripts used for the build are available here:
https://github.com/saezlab/Meta_PKN 

This material is part of a manuscript under submission.

In case of any question please contact Aurelien Dugourd 
aurelien.dugourd@bioquant.uni-heidelberg.de

Format
------

- The `X` prefix has the only purpose of avoiding automatic
  conversion to number format in spreadsheet software, it
  can be safely removed
- Proteins are encoded by Entrez Gene IDs
- Genes from the recon3D reaction network are prefixed with
  Gene###. The actual NCBI gene identifier can be found after
  the “__” separator.
- In the recon3D part of the network, complexes can be found
  in the form __###_###_### where each separate number is a
  NCBI gene identifier
- Metabolites are encoded by PubChem CIDs and prefixed
  with the `Metab__` label
- When no identifiers where available in pubchem or NCBI,
  original recon3d identifiers and gene/reaction names were
  kept.