Transcript Gene Expression Analysis - BC Bioinformatics

BI420 – Introduction to Bioinformatics
Gene Expression Analysis
Gabor T. Marth
Department of Biology, Boston College
[email protected]
Gene expression
Why study gene expression?
Which genes are active
• at different developmental stages?
• in cells of different tissues?
• at different time points in the same cell?
• cells under different environmental conditions?
• between normal and cancerous cells?
What are expression microarrays?
Expression microarrays – “physical appearance”
Microarray construction
cDNA preparation
Expression assay
Expression microarray movie
DNA microarray chip animation:
http://www.bio.davidson.edu/Courses/genomics/chip/chip.html
Chip readout – absolute expression and ratio
Chip readout – relative transcription
Chip readout – example
Time course experiments
Experiment: measuring
gene expression as
oxygen gets depleted
in yeast grown in a
closed container
Time course data
Data analysis – normalization
• balance fluorescent intensities of two dyes
• adjust for differences in experimental conditions
Normalization
Log2 transformation
Double or half expression now
has the same magnitude
Clustering – intro
• Why: if the expression pattern
for gene B is similar to gene A,
maybe they are involved in the
same or related pathway
• How: Re-order expression
vectors in the data set so that
similar patterns are together
Clustering – numerical
Clustering – visual
Hierarchical clustering: pair-wise similarity
Hierarchical clustering: cluster construction
Clustering – large example
Next two classes
Chapter 7.
Chapter 8.
Application of microarrays: classification of cancers
Microarrays to detect genome copy #
Protein identification
Protein separation by 2D gel eletrophoresis
Protein identification
mass spectrometry
Protein function identification
protein chips: identification of proteins that bind
specific chemicals
Thanks
Expression informatics slides courtesy of:
Olga Troyanskaya, Ph.D.
Department of Computer Science
Lewis-Sigler Institute for Integrative Genomics
Princeton University