Bioinformatics: Week 1 Part 2

Question 1

Microarrays

Answer 1

Microarrays - study gene expression

> ssDNA probes are immobilized on a substrate in a discrete location with spots
Target DNA is labelled with a fluorophore and hybridized to the array

The intensity of the signal is used to determine the number of bound molecules.

Question 2

1.1 Commercial Microarrays

Answer 2

✓ Unlike Custom Arrays, hybridization is pre-set + no colour change, but a grey scale

available in different sets
most common known one is - affymetrix

grey scale

Question 3

1.2 Custom microarrays

Answer 3

> .cDNA (clonal DNA) from ESTs (Expressed sequence tags)
✓ EST = originates from expressed sequence tags
Work with cDNA clones which originate from express sequence tags
> Two samples
§ Control and experimental sample
> Each spot on the array has a specific cDNA
> Colour
§ Green - down regulated
§ Red - up regulated

Question 4

1.3 Custom Arrays vs Commercial Arrays

Answer 4

Custom:

• Cheap
• Limited samples by choice
• Technically difficult
• Technical variability big
• Must have access to probes and sequences
• Error margin big

Commercial Array

• Expensive
• Large sample size
• Technically easy, set methodology
• Technical Variation small
• Probes and sequences are available, part of the slide
• Error margin small

Question 5

1.4 Difference in steps between commercial and custom

Answer 5

look on objective - table