Bioinformatics Coursework:

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1 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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Course 341: Introduction to Bioinformatics

Microarray Bioinformatics Tutorial 1

(Review questions on gene expression)


1.

What is meant by gene expression?


2.

Why are microarrays a hot topic in bioinformatics?


3.

What do we mean by the term “Gene co
-
expression”,

and how can microarrays be
used to study co
-
expressed genes.


4.

How can microarrays be used to study the relationships between different disease
types?


5.

Explain briefly how microarray experiments can be used in different phases of the
drug discovery process
.


(Review questions on microarray technology)


6.

Explain the basic idea behind microarrays.


7.

When manufacturing microarrays:


a)

What are the main two types of probes that can be used and what are the
advantages of each?


b)

What is the difference between spotti
ng and in
-
situ synthesis and what are the
advantages of each?


8.

Describe the difference between single
-
label experiments and dual label experiments.
What are the data analysis implications of each?


9.

Describe the operation of cDNA microarrays. Make sure you
solutions explains the
interpretation of the colours “Red”, “Yellow” and “Green”.


10.

Describe the Affymetrix microarray technology.




Make sure your answer defines the term “oligonucleotides” and describes how
“photodeprotection using masks” is used to fix t
he oligonucleotide probes to the
to the array surface.



Make sure your answer describes what is meant by a “Probe”, “Probe Pair” and
“Probe Set”.



Make sure that you answer describes the terms “Perfect Match Probe”, and
“Mismatch Probe” and how they are used
.


11.

What is the general workflow for conducting a microarray experiment? Make sure
your answer describes both manufacturing the array and using it.


12.

What are the main steps in the analysis of microarray data and what are the main
data structures used?


13.

Des
cribe what type of image processing may be required for reading a microarray
output, giving examples of typical problems need to be addressed.


14.

What is meant by gene expression matrix and how it can be generated from a raw
microarray data.


(Problems)


15.

Usi
ng a series of diagrams, show how the following the following probes “GTGT” and
“ATAT” can be in
-
situ
-
synthesized on an array surface using the affymetrix approach.