Mapping the Genotype–Phenotype Relationship in Cellular Signaling Networks: Building Bridges Over the Unknown - Systems Biology: Networks, Models, and Applications - page 142

or the chemical transformations that comprise a network

Name Description Advantages Disadvantages References

Bioinformatics sequence Indicates the function of Takes advantage of the Relies upon existing data, [25,26]

analysis specific proteins by large amount of data that which is not necessarily always

searching for sequence is already available, and the accurate, i.e., the prediction

homologies. An increasing vast supply of computational is only as good as the original

number of approaches resources. assignment.

synthesize multiple data Very efficient. Does not provide any “new”

sources to predict protein discoveries, in the sense that

function. proteins with no sequence

homologies or structure
similarities remain difficult
to reconcile.

Coimmunoprecipitation Indicates which proteins Enables the unbiased testing May generate false positives [27-29]

interact with one another. of multiple ligands against for proteins in a complex that

Like immunoprecipitation, a specific target protein. do not directly interact.

this technique is based on Protein concentrations, Level of sensitivity is less

the formation of immune posttranslational than that of other methods

complexes: a cell lysate is modifications, and other because the antigen

produced; the protein of in vivo characteristics concentration is inherently

interest is tagged by an are more likely to be lower to avoid banding of

antibody; the antigen is maintained. the antibodies. There are

added and allowed to ways to overcome this pitfall,

precipitate with the protein but these usually result in

antibody (and thereby perturbations of the simulated

“coprecipitate” with any natural environment.