*The main criticism applied to the yeast two-hybrid screen of protein–protein interactions are the possibility of a high number of false positive (and false negative) identifications. The exact rate of false positive results is not known, but earlier estimates were as high as 70%. This also, partly, explains the often found very small overlap in results when using a (high throughput) two-hybrid screening, especially when using different experimental systems.
The reason for this high error rate lies in the characteristics of the screen:
*Certain assay variants overexpress the fusion proteins which may cause unnatural protein concentrations that lead to unspecific (false) positives.
*The hybrid proteins are fusion proteins; that is, the fused parts may inhibit certain interactions, especially if an interaction takes place at the N-terminus of a test protein (where the DNA-binding or activation domain is typically attached).
*An interaction may not happen in yeast, the typical host organism for Y2H. For instance, if a bacterial protein is tested in yeast, it may lack a chaperone for proper folding that is only present in its bacterial host. Moreover, a mammalian protein is sometimes not correctly modified in yeast (e.g., missing phosphorylation), which can also lead to false results.
*The Y2H takes place in the nucleus. If test proteins are not localized to the nucleus (because they have other localization signals) two interacting proteins may be found to be non-interacting.
*Some proteins might specifically interact when they are co-expressed in the yeast, although in reality they are never present in the same cell at the same time. However, in most cases it cannot be ruled out that such proteins are indeed expressed in certain cells or under certain circumstances.
Each of these points alone can give rise to false results. Due to the combined effects of all error sources yeast two-hybrid have to be interpreted with caution. The probability of generating false positives means that all interactions should be confirmed by a high confidence assay, for example co-immunoprecipitation of the endogenous proteins, which is difficult for large scale protein–protein interaction data. Alternatively, Y2H data can be verified using multiple Y2H variants or bioinformatics techniques. The latter test whether interacting proteins are expressed at the same time, share some common features (such as gene ontology annotations or certain network topologies), have homologous interactions in other species.