Mapping the Genotype–Phenotype Relationship in Cellular Signaling Networks: Building Bridges Over the Unknown - Systems Biology: Networks, Models, and Applications - page 136

Figure 5.1 Mapping genotype-phenotype relationships in cellular signaling
networks. Various experimental technologies have been developed to elucidate
information about the properties of cellular signaling networks. Here a portrait is
provided of the specific activities and reactions that are characterized by different
techniques. Specifically, in Tier I, four examples of technologies that enable the
identification of the genotype are illustrated: chromatin immunoprecipitation
(ChIP) (1) and chromatin immunoprecipitation with microarrays (ChIP-chip) (2)
indicate which proteins bind to DNA sequences in vivo; microarrays (3) show
which genes are expressed, i.e., transcribed into RNA; and genome sequencing (4)
identifies all the base pairs contained in a genome. Tier II encompasses the
technologies that characterize intermediate phenotypes, or the chemical
transformations that comprise a cellular signaling network: coimmunopre-
cipitation (5), fluorescent resonance energy transfer (FRET)-based techniques (8),
and (yeast) two-hybrid assays (16) indicate which proteins interact with one
another; crosslinking (6) and mass spectrometry (MS)-based techniques (10)
specify the composition of protein complexes; phage display (12), protein affinity
chromatography (13), and protein probing (14) indicate which proteins bind to
specific targets; microarrays (7) indicate the phenotypic function of a set of genes;
and gene knockouts (9), mutagenesis assays (11), and RNA interference (RNAi)
(15) generate data about various genes by altering normal cellular activity
through gene deletions, genetic mutations, and inhibition of RNA transcription,
respectively. Finally, Tier III consists of technologies that provide data about
the endpoint phenotypes, or the transcriptional and cellular modifications as a
result of intermediate phenotypes: the Boyden filter transmigration assay (17),
Dunn chemotaxis chamber (18), and Zigmund chamber (22) offer quantitative
assessment of cellular migration, a cell-scale property; flow cytometry (19) is a
technique for counting the number of cells within a given population (e.g., to
assess the rate of cell division); and the microplate reader (21) provides dynamic
growth-rate measurements of many different cell cultures simultaneously.
Assimilating all of the data generated by these experimental technologies may
provide understanding and enable modeling of cellular signaling networks (20).
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