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Ten thousand random sets of 25 genes (same number as genetic interactions annotated in BioGRID among our mutant hits) were checked for annotated genetic interactions.
In this article, we designed a semi-supervised multi-task learning framework to integrate a larger set of potentially interacting protein pairs retrieved from literature (weak labels) and a smaller set of interactions annotated by experts.
Mutants within the Rosetta compendium may be associated by common KEGG category (71 mutant experiments) or by protein-protein interactions annotated in MIPS PPI (30 mutant experiments).
A similar approach using the published genetic and proteomic interactions annotated within the SGD identified five DOX resistance genes that were not detected in the primary screen and exhibited an intermediate sensitivity to DOX induced cytotoxicity (Fig. 4).
For positive genetic interactions, interactions annotated as phenotypic suppression and synthetic rescue are used.
Possible exceptions are human interactions annotated by HPRD, which have ambiguous detection method labels.
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This term proved to be too ambiguous to adequately describe the interaction annotated in major interaction databases, and unpopular with users, so it was made obsolete.
Interactions were annotated as HIGH if both proteins were annotated HIGH or a combination of HIGH-MEDIUM or HIGH-LO W MEDIUM if both proteins were annotated MEDIUM or MEDIUM-LO W and LOW if both proteins were annotated LOW.
Additionally, 55% of the interactions were annotated as HIGH, 35% as MEDIUM and 10% annotated as LOW, indicating the relevance of the network with respect to CRC.
Self interactions are annotated as binary interactions with the same participant.
Interactions are annotated with supporting information, such as interaction type, experimental detection methods and supporting publications.
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