reactome — Reactome human protein interactions (2014)
- Description
A network of interactions between human proteins, derived from Reactome, an open, manually curated database of biological pathways and reactions. Nodes are proteins (UniProt entries, including isoforms) and an undirected edge connects two proteins that Reactome's curators annotated as taking part in the same complex or reaction; the interactions are thus inferred from the pathway annotations ("inferred by curator", in the PSI-MI vocabulary), rather than measured directly. Some proteins interact with themselves, and appear with self-loops. This is the Reactome protein–protein interaction file for Homo sapiens in PSI-MITAB format as it was distributed by Reactome in August 2014; Reactome has since changed considerably.
The network has the following properties:
- Nodes:
uniprot, the UniProt accession of the protein (with an isoform suffix where applicable);name, the short label (gene name) of the protein, empty if not given in the data. - Edges:
interaction_type, the PSI-MI interaction type,physical associationorassociation;pathways,reactions,complexesandregulations, the lists of the Reactome stable identifiers of the pathways, reactions, complexes or polymers, and regulations in which the interaction was found (in the identifier scheme of that time,REACT_*). In the data, complexes are only given for physical associations, and regulations only for associations.
- Nodes:
- Tags
- Biological Protein interactions Unweighted Metadata
- Citation
-
- G. Joshi-Tope et al., "Reactome: a knowledgebase of biological pathways." Nucleic Acids Research 33(suppl. 1), D428-D432 (2005) 10.1093/nar/gki072 Sci-Hub
- I. Vastrik, P. D'Eustachio, E. Schmidt, G. Joshi-Tope, G. Gopinath, D. Croft, B. de Bono, M. Gillespie, B. Jassal, S. Lewis, L. Matthews, G. Wu, E. Birney, L. Stein, "Reactome: a knowledge base of biologic pathways and processes." Genome Biology 8(3), R39 (2007) 10.1186/gb-2007-8-3-r39 Sci-Hub
- Upstream URL OK
- https://reactome.org/download-data
- Upstream license
- CC BY 4.0, https://reactome.org/license
- Networks
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Tip: hover over a column header 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
- Ridiculograms*
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