Lecture 4 FInal Flashcards
_______ is a complex network in which the components are connected functionally
a cell
What are the rough four steps of genomic analysis
- Genomic/transcription
- metabolic pathway regulatory motif
- Functional modules
- Large Scale Networks
What are some of the biological networks
- Evolutionary Tree of life
- Ecological networks
- Expression networks (based on gene expression patterns)
- Regulatory networks (based on gene regulation)
- Protein interaction
- The metabolic network in cells
Why are proteins-protein interactions so important?
The binding of one signal protein to another can have 2 number of consequences
- recruitment
- conformational change
What are the experimental methods are important to understand protein interactions
- yeast two hybrid
- tagged fusion
- communoprecipitation
- protein-protein array
Basic principle of ____________ activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activity sequencing (UAS)
Two Hybrid system
Modular domains of transcription factors
(domains of the gene can be taken out and they function on their own)
Gene expression is continuous by the binding of protein __________
to the promotor regions (UAS)
__________ is a known protein the investigator is using to identify new binding partners (candidate binding partners are called prey proteins)
Bait Protein (Two hybrid systeem)
_____________ candidate binding proteins. Both proteins are expressed in a yeast cell that carries a sepereate gene whose expression is under the control of binding site for the DNA binding domain
prey protein
Th two hybrid system:
interaction _________ localizes ___________ to the reporter gene (activating transcription)
of bait and prey protein
the activation domain
___________ easy applicable to high throughout the PPI screens by designing large numbers of combinations of prey and bait proteins
-survival selection:
Biological network:
__________ genes, proteins, peptides, or non protein biomolecule
nodes
Biological network:
_____________ biological relationship and interactions regulations
edges
IT is usually represented by a 2D diagram with characteristic symbols linking to the protein and non protein entities
Biological networks
- circle indicates a protein/ non protein biomolecule
- symbol between indicates the nature of molecule-molecule interactions
The color of a node signifies the ________________
phenotype affected of remaining the corresponding proteins
The yeast protein interaction
tends to reveal some basic graph theoretic properties
-The frequency of protein having interactions with exactly _______________________
k other proteins follow a power line
The network exhibits the _________ can reach any node within small number of hops
small world phenomenon
_____________ is resilient and have strong resistance to failure on random attacks and vulnerable to targeted attacks
robustness
Degree and conductivity K of node:
- unidirectional
- bidirectional
_____________- the probability that a selected node has exactly K links P(K)
degree distribution
*calculated based on the known network structure
_______is obtained by counting the number of nodes N(k) with links divided by the number o nodes
-P(k)
_____________ the probability of finding a highly connected node decreases exponentially with K; is a constant different for different networks
scale free network
