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Fig. 1. Experiments that establish relationships between genes, proteins, cells
and functions. Most genome-wide data sets describe biological entities or
draw connections between entities. For example, DNA sequence is linked to
genes by gene prediction and experimental annotation (e.g. cDNA sequencing).
Genes are associated with other genes by genetic interactions. Proteins are
related by physical binding, e.g. as detected in yeast two-hybrid assays.
Proteins are shown to interact with DNA through chromatin-immunoprecipitation
(ChIP) and yeast one-hybrid assays (e.g.
Deplancke et al., 2006). Genes
and protein are assigned functions based on perturbations (mutations,
overexpression, RNAi). Cells are associated with genes and proteins by gene
expression. Cells (or tissues) are associated with functions by mechanical
(e.g. laser ablation) or genetic (e.g. mutation) lesion experiments or by
generating genetic mosaics.
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