Mapping the Genotype–Phenotype Relationship in Cellular Signaling Networks: Building Bridges Over the Unknown - Systems Biology: Networks, Models, and Applications - page 138

genes of a genome

Name Description Advantages Disadvantages References

Chromatin Indicates whether a specific Is performed in vivo. Precipitation is often inefficient, [2,3]

immuno- protein binds to a specific i.e., insufficient protein is

precipitation DNA sequence in vivo. Cells recovered.

(ChIP) are grown under native Crosslinking may require

conditions, and are purification of the DNA-protein

subsequently fixed with complex, which can be tedious

formaldehyde so that the and expensive.

transcription factor proteins Crosslinking may fix interactions

crosslink with the chromatin. that are transient and/or of

The genomic DNA, bound to minor significance.

the transcription factors, is Suspected genetic targets

then sheared into appropriately must be predefined.

sized fragments. These are Significant quantities of

immunoprecipitated to fragmented DNA must be

determine the binding domains. available.

Chromatin Provides the comprehensive Enables the Various technical aspects of the [4-8]

immunoprecipitation identification of all targets of a identification, in a procedure remain difficult to

with microarray transcription factor within a single experiment, control, including fixation,

analysis (ChIP-chip) genome. Bound DNA fragments of all the targets of epitope accessibility, antibody

are recovered and hybridized a transcription specificity, and choice of

to a chip consisting of all the factor. microarray content.

regulatory regions within Prior knowledge of

the genome. potential binding sites

is not needed, since