The full characterization of the peptide recognition specificity of the different members of the PTP family and the completion of projects aimed at a higher coverage of the interactions mediated by phosphatases will allow the application of this strategy to a larger number of tyrosine phosphatases.
Although there are some variations in the read coverage of the individual interactions, similar interactions can be observed by both 4C-seq and T2C.
In particular, efficient bioinformatics procedures enabling integrative analysis of multiple datasets from various screening approaches could increase the quality and coverage of the genetic interaction maps, with the aim of completing the genetic interaction networks in yeast and other organisms.
To estimate the coverage of the protein interaction network achieved so far, we undertook a curation effort to capture from the literature a large fraction of the interactions in which at least one of the partners is one of the 255 phosphatases or regulatory subunits in our compendium.
The coverage of the extracellular interaction network is not complete and MatrixDB is regularly updated.
As currently the coverage of the protein interaction network is limited, we suggest performing MATISSE analysis in addition to standard clustering analysis.
In general, such computational approach can facilitate the experimental efforts by improving the quality and coverage of the current genetic interaction networks, towards completing the still incomplete information of genetic interactions in yeast, which is - by and large - complementary to that obtained from the physical protein interactions and complexes [ 1, 5, 11, 17, 39, 40].
This may be due to evolutionary divergence or to differences between the current coverage of the two organisms' interaction maps.
Nevertheless, there is a large variation in the coverage of protein interaction data across the interaction databases [ 70].
The tumor cells showed a distinct higher coverage of the original protein-interaction network for these pathways.
