Week 6

Question 1

What crosstalk signaling pathways entail?

Answer 1

Crosstalk occurs between two signaling pathways A and B when the stimulation at the receptors of pathway A causes a cellular response downstream of pathway B, usually carried out by the TFs in B.

Question 2

What is nuclear receptor crosstalk?

Answer 2

The interplay between different nuclear receptors or between their overlapping signalling pathways

Question 3

Where do toll-like receptors (TLRs) 4, 5, 7 and 9 belong to?

Answer 3

A family of proteins that recognize mainly conserved microbial motifs

Question 4

What does Kaposi’s sarcoma-associated herpesvirus interact with?

Answer 4

Cell surface receptors, such as heparan sulfate, integrins (α3β1, αVβ3, and αVβ5), and EphrinA2 (EphA2), and activates focal adhesion kinase (FAK), Src, phosphoinositol 3-kinase (PI3-K), c-Cbl, and RhoA GTPase signal molecules early during lipid raft (LR)-dependent productive macropinocytic entry into human dermal microvascular endothelial cells

Question 5

What are two types of crosstalk?

Answer 5

The two types of crosstalk are near-end and far-end crosstalk, both of which create unwanted interference between signals on different interconnects

Question 6

What are some limitations of a graph?

Answer 6

No more than two measurement types can be displayed on a graph

Question 7

What is a central issue in systems biology?

Answer 7

Understanding signal transduction in cellular systems

Question 8

What can discrete dynamic modeling, combined with network analysis provide?

Answer 8

An effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters

Question 9

What is the advantages of dynamic model?

Answer 9

Although some complex systems may be difficult to model accurately, dynamic modeling provides extra product performance data from virtual prototypes

Question 10

What is a critical challenge for cancer therapy?

Answer 10

Prediction of drug combinations that effectively target cancer cells

Question 11

What can the analysis of signalling network activity and crosstalk predict?

Answer 11

Potent drug combinations and rational stratification of patients, thus bringing therapeutic and prognostic values. We have previously showed that the non-receptor tyrosine kinase PYK2 is a downstream effector of EGFR and c-Met and demonstrated their crosstalk signalling in basal-like TNBC

Question 12

How does the iterative modeling approach work?

Answer 12

The same logical steps may be repeated by using different software, or different versions of the same software, with or without additional data

Question 13

What models are used in biology?

Answer 13

After reflecting on the types of models we use in our daily work as biological researchers, we have identified three main categories of models used regularly in scientific practice: concrete, conceptual, and mathematical

Question 14

What are the major computational approaches used to study signaling networks?

Answer 14

Graph theory and dynamical modeling

Question 15

What is network theory?

Answer 15

A network can be defined as a graph in which nodes and/or edges have attributes

Question 16

What are the different types of signalling?

Answer 16

There are four basic categories of chemical signaling found in multicellular organisms: paracrine signaling, autocrine signaling, endocrine signaling, and signaling by direct contact.

Question 17

What are hubs?

Answer 17

They represent proteins with a large number of interactions

Question 18

What are clusters?

Answer 18

Tightly linked sets of mostly non-homologous genes participating in a common, discrete metabolic pathway

Question 19

What is a path?

Answer 19

A step by step series of interconnected biochemical reactions in which each step is catalyzed by a specific enzyme

Question 20

Where does Ras activates it’s effectors?

Answer 20

At the membrane

Question 21

Where does active PI3K-alpha assemble?

Answer 21

At membrane regions enriched in signaling lipids

Question 22

Where does the the Raf kinase domain localise?

Answer 22

It extends into the cytoplasm and its assembly is away from the crowded membrane surface

Question 23

What is network visualisation?

Answer 23

Network visualization, graph visualization or link analysis is the process of visually presenting networks of connected entities as links and nodes

Question 24

What is network clustering?

Answer 24

Network clustering (or graph clustering) refers to both a computational problem to extract densely connected but relatively isolated subnetworks from a network and a set of algorithms and methods to solve this problem

Question 25

What is crucial in treating the signal flow of complex diseases?

Answer 25

Identifying control targets that can most effectively block such unwanted signal flow

Question 26

What are examples of spatial information?

Answer 26

Data includes spatial information such as spatial coordinates for land boundaries, area or size, road and street names, names of waterways, codes for local government.

Question 27

What are regulatory motifs?

Answer 27

Short nucleotide sequences typically upstream of genes that are used to control the expression of genes

Question 28

What are positive and negative feedback loops?

Answer 28

Common regulatory elements in biological signaling systems

Question 29

What is Hippo YAP?

Answer 29

A complex network of proteins that controls organ size via regulation of cellular proliferation, survival and differentiation

Question 30

What does PI3K-Akt do?

Answer 30

Promotes metabolism, proliferation, cell survival, growth and angiogenesis in response to extracellular signals

Question 31

What does Ras do in the MAPK pathway?

Answer 31

Transduce signals from the extracellular milieu to the cell nucleus where specific genes are activated for cell growth, division and differentiation