genesbyproteinproteininteraction: Find interacting partners of a specific gene as determined by...
In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description Arguments Value

Find interacting partners of a specific gene as determined by yeast two-hybrid experiments. This data is available for P. falciparum only. 'Number of searches that found this interaction' or Times reproduced refers to the number of independent yeast two-hybrid screens in which a given interaction was found. Interactions found in two or more yeast two-hybrid screens were independently reproduced, and are thus more likely to be true yeast two-hybrid positives. 'Number of times this interaction was found' or Times observed refers to the total number of times a given interaction was identified in all yeast two-hybrid screens. An interaction can be identified multiple times in the same screen for several reasons: (1) The original yeast cell containing the pair of interacting proteins divided before being plated on selective media; (2) The same prey plasmid was present in the library multiple times and thus gave rise to multiple positive colonies; or (3) The prey gene was present in the library as multiple independent, overlapping fragments, all of which interact with a given bait. Only (3) provides independent confirmation of a putative interaction. Protein interactions were experimentally determined using the yeast two-hybrid system as described in LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE. A protein interaction network of the malaria parasite Plasmodium falciparum. <a href="http://www.ncbi.nlm.nih.gov/pubmed/16267556">Nature. 2005 438:103-7</a>.

`organism`	Organism Provide one or more values. Use comma as a delimter.
`single_gene_id`	Gene IDs (locus tags) are quite different for each species. We use the gene IDs provided by the sequence generator.
`min_searches`	Restrict by the minimum number of searches that found this interaction
`min_observed`	Restrict by the minimum number of times this interaction was found
`bait_or_prey`	Optionally specifiy whether given protein is bait or prey
`o-fields`	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`o-tables`	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`.convert`	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and `TRUE`, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is `FALSE`, the value from the Web server is returned as is.
`.url`	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
`.json`	a logical value controlling whether to use the JSON or the XML version of the method