Chapter 4 - Temporal programs and global structure of transcription networks Flashcards
What does SIM stand for?
Single-input module
What is a SIM:
A network motif that is made up of one master transcription factor that regulates a bunch of genes with only the master transcription factor as input. The regulation sign is the same for alle the genes. The master transcription factor usually also autoregulatory.
What are the function of SIM genes?
They alle have similar functions - they are involved in the same pathway.
How can SIMs generate temporal programs of expression?
By having different activation thresholds for the different genes regulated by the master TF.
When are SIMs used?
1) Metabolic pathways
2) Stress (DNA)
3) Advanced proteins (e.g. the ribosome)
Most important SIM function:
To control a group of genes sensed by the master transcription factor.
What is LIFO?
Last in first out
What is just-in-time-production?
When genes are produced just as they are needed as a result of temporal programs of expression.
FIFO?
First in first out
How to obtain FIFO?
Through mutli-output FFLs.
Why do we stop at 4 node subgraphs?
Because all higher order networks can be build out of 4 node subgraphs.
What are the two significant 4 node FFLs?
1) two output FFL
2) Bi fan
What is the multiple output FFL?
X -> Y -> Z1, … , Zn but also X -> Z1, … , Zn
Made out of Two output FFLs.
What is LIFO?
Last in first out.
What is a SUM gate?
Where the response is a sum of more transcription factors. E.g. the weigthed sum of the TFs has to be over a threshold. This is how LIFO is generated and can also be seen as an OR gate with different activation constants.
