Criticisms.2C challenges.2C and responses Interactome

kiemer , cesareni raise following concerns state (circa 2007) of field comparative interactomic: experimental procedures associated field error prone leading noisy results . leads 30% of reported interactions being artifacts. in fact, 2 groups using same techniques on same organism found less 30% interactions in common. however, authors have argued such non-reproducibility results extraordinary sensitivity of various methods small experimental variation. instance, identical conditions in y2h assays result in different interactions when different y2h vectors used.

techniques may biased, i.e. technique determines interactions found. in fact, method has built in biases, protein methods. because every protein different no method can capture properties of each protein. instance, analytical methods work fine soluble proteins deal poorly membrane proteins. true y2h , ap/ms technologies.

interactomes not complete perhaps exception of s. cerevisiae. not criticism scientific area incomplete until methodologies have been improved. interactomics in 2015 genome sequencing in late 1990s, given few interactome datasets available (see table above).

while genomes stable, interactomes may vary between tissues, cell types, , developmental stages. again, not criticism, rather description of challenges in field.

it difficult match evolutionarily related proteins in distantly related species. while homologous dna sequences can found relatively easily, more difficult predict homologous interactions ( interologs ) because homologs of 2 interacting proteins not need interact. instance, within proteome 2 proteins may interact paralogs may not.

each protein–protein interactome may represent partial sample of potential interactions, when supposedly definitive version published in scientific journal. additional factors may have roles in protein interactions have yet incorporated in interactomes. binding strength of various protein interactors, microenvironmental factors, sensitivity various procedures, , physiological state of cell impact protein–protein interactions, yet not accounted in interactome studies.