Information Technology Reference
In-Depth Information
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TF
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4
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Regulatory Coexpression
a)
TF
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TF
TF
Combinatorial
b)
Fig. 2.2. a) Schematic view of the direct correspondence existing between regulatory and co-
expression network in a simple case of regulation: the TF is the only regulator of genes 1 to 4
and moreover it has a positive eect on the expression of each of them. In this case genes 1 to 4
have highly correlated gene expression proles and thus form a tight cluster in the coexpression
network. This is true in Bacteria, where combinatorial promoters are less common. b) In most
eukaryotes combinatorial promoters (i.e. promoters controlled by more transcription factors) can
be common, making this relationship less clear and often dynamic (the expression of dierent TF
in time could mean that dierent coexpression groups can be formed from the same set of genes).
A scheme of the basic approach is measuring mRNA levels in a cell culture in two
dierent conditions. One of the two is intended as a control, the other as a treated
sample. The treatment is here intended in the general sense of a perturbation of
the original system, i.e. presence of a given compound in the culture medium or a
genetic alteration, so that it is possible to monitor the genes signicantly changing
their expression levels with respect to the control situation. Genes that are more
expressed in the treated sample can be further analyzed with the idea in mind that
they have a function related to the treatment. Schematically total mRNA is ex-
