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stitch_chemicals — STITCH chemical-chemical and protein-chemical associations (2015)

Description

Networks of known and predicted associations between chemicals, and between chemicals and proteins, from STITCH ("search tool for interactions of chemicals"), version 5.0, the companion database of STRING (see the entries string_all and string_ppi). The chemicals are those of PubChem; STITCH merges the salt forms of a compound, and distinguishes the stereo-specific compounds (identifiers CIDs...) from the "flat" compounds whose stereoisomers are merged (CIDm...); the suffix is the PubChem compound identifier (CID). The proteins are those of STRING 10.

STITCH combines evidence from several channels, each of which gives a confidence score, into a combined confidence score: experiments (e.g. binding affinities from ChEMBL, PDSP Ki, PDB), curated databases (e.g. DrugBank, KEGG, GLIDA, Matador, CTD), co-mention in the scientific literature (text mining), and, for protein-chemical links, predictions (e.g. from co-occurrence in pathways), and, for chemical-chemical links, the structural similarity of the chemicals. Scores are multiplied by 1000 (the lowest combined score in the files is 150).

  • chemical_chemical: an undirected network of chemicals, with an edge between two associated chemicals (both orientations of each pair are listed upstream; each pair is an edge once). A few chemicals (34) are associated with themselves, as self-loops.
  • protein_chemical_<taxid>: a bipartite network of the chemicals and the proteins of an organism, with an edge between a chemical and a protein associated with it. STITCH has such networks for 2,031 organisms (31 GB of files); only those of the seven model organisms of the entry string_ppi are included, named after their NCBI taxonomy identifiers: 9606 (human), 10090 (mouse), 4932 (yeast Saccharomyces cerevisiae), 511145 (Escherichia coli K-12 MG1655), 7227 (fruit fly Drosophila melanogaster), 6239 (Caenorhabditis elegans) and 3702 (Arabidopsis thaliana).

Left out are the associations transferred between organisms by orthology (a separate file of STITCH), and the modes of action (activation, inhibition, binding, ...), which are only available for a subset of the associations.

The networks have the following properties:

  • stitch_id: the identifier of the node in STITCH: CIDm<CID> or CIDs<CID> (with the CID padded with zeros to 8 digits) for chemicals, <taxid>.<protein id> (e.g. 9606.ENSP00000257254) for proteins.
  • name: the name of the chemical (empty for proteins).
  • molecular_weight: the molecular weight of the chemical (NaN for proteins).
  • smiles: the structure of the chemical, as a SMILES string (empty for proteins).
  • is_chemical (protein_chemical_<taxid> networks): whether the node is a chemical (otherwise it is a protein).
  • Edge combined_score: the combined confidence score of the association (from 150 to 999).
  • Edge experimental, database, textmining: the scores of the corresponding channels (0 if there is no evidence of that kind).
  • Edge similarity (chemical_chemical): the score of the structural similarity of the chemicals.
  • Edge prediction (protein_chemical_<taxid>): the score of the predictions.
  • taxon_id, organism (graph, protein_chemical_<taxid>): the NCBI taxonomy identifier and the name of the organism.
Tags
Biological Chemical Drug interactions Weighted Metadata
Citation
  • D. Szklarczyk, A. Santos, C. von Mering, L. J. Jensen, P. Bork, M. Kuhn, "STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data." Nucleic Acids Research 44, D380-D384 (2016) 10.1093/nar/gkv1277 Sci-Hub
Upstream URL OK
http://stitch-db.org/cgi/download.pl
Upstream license
CC BY-NC-SA 4.0 (detailed scores; the combined scores and the chemicals are CC BY 4.0), http://creativecommons.org/licenses/by-nc-sa/4.0/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
chemical_chemical 389,393 8,852,926 45.47 122.69 579.25 2790707.19 0.06 0.10 14 0.99 Undirected Unipartite stitch_id name molecular_weight smiles similarity experimental database textmining combined_score 42.1 MiB 75.2 MiB 71.8 MiB 69.1 MiB
protein_chemical_9606 806,234 15,473,939 38.39 659.94 2692.45 51.29 -0.36 0.00 8 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 40.8 MiB 95.4 MiB 92.8 MiB 92.6 MiB
protein_chemical_10090 799,456 39,116,252 97.86 1787.79 4496.09 57.21 -0.43 0.00 7 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 53.6 MiB 186.1 MiB 178.9 MiB 175.6 MiB
protein_chemical_4932 317,735 3,533,097 22.24 262.02 674.13 29.49 -0.17 0.00 7 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 9.9 MiB 27.6 MiB 26.9 MiB 27.3 MiB
protein_chemical_511145 152,443 2,278,768 29.90 143.59 386.15 28.51 -0.36 0.00 6 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 5.5 MiB 17.7 MiB 17.1 MiB 16.7 MiB
protein_chemical_7227 655,591 20,087,229 61.28 1282.15 2691.81 63.03 -0.31 0.00 8 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 30.9 MiB 100.3 MiB 97.0 MiB 97.3 MiB
protein_chemical_6239 648,386 25,946,333 80.03 1553.48 3323.59 73.18 -0.36 0.00 7 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 33.1 MiB 121.3 MiB 115.4 MiB 115.9 MiB
protein_chemical_3702 342,680 23,546,245 137.42 916.20 3399.74 27.51 -0.48 0.00 8 1.00 Undirected Bipartite stitch_id is_chemical name molecular_weight smiles experimental prediction database textmining combined_score 30.4 MiB 103.9 MiB 104.4 MiB 96.0 MiB