string数据库

What does the columns in proteins.actions file mean? Top ↑

Here is a brief explanation of the column names for the action evidence.

• item_id_a - identifier of protein A
• item_id_b - identifier of protein B
• mode - type of interaction (e.g. "reaction", "expression", "activation", "ptmod"(post-translational modifications), "binding", "catalysis")
• action - the effect of the action ("inhibition", "activation")
• a_is_acting - the directionality of the action if applicable ('t' gives that item_id_a is acting upon item_id_b)
• is_directional - describes if the diractionality of the particular interaction is known.
• score - the combined score of all interactions in string.
• source - describes the source of inferred interaction is taken (bind, biocarta, biocyc, dip, grid, hprd, intact, kegg_pathways, mint, pdb, PID, reactome).
• transferred_sources - Sources used for transfer of evidence by homology/orthology from another species. (if two proteins are interacting in several other species it is plausible that it is interacting in close species where it has not been observed).

How do I import several interactions from STRING into Cytoscape. Top ↑

Cytoscape supports "tab separated values" file format. Download the "protein.links file" (from STRING download page), extract the interactions for you want (use grep or copy-paste), and load the processed file into cytoscape