1. Overview Expression data basics Introduction Biological network data
Text mining
Gene Ontology
Expression data basics
Expression, text mining, and GO
Modules and complexes
Domains and conclusion

2. Key points on expression data
What genes are in the genome doesn’t matter as much as how and when they are used.
Microarray technology is global; we can measure expression of all genes with one experiment.
Microarray results are noisy.

3. From: http://www.bioteach.ubc.ca/MolecularBiology/microarray/
Expression Arrays
From:
Standard technology for measuring mRNA expression
Global, repeatable, quantitative.
Analysis methods are well-understood, widely available.
mRNA abundances do not reflect protein abundances or states.

4. Oligonucleotide Arrays (Shown: Affymetrix arrays)
Millions of identical probes / feature *
Photolithography
UV light
Mask
1.28cm
Substrate
We talk a lot about "wafers", "chips", and "features". This is a graphical representation.
We've mirrored the technology in the semiconductor industry, photolithography, with life sciences.
We do manufacture on wafers. These wafers are 5-inch-by-5-inch pieces of glass.
In our whole-genome products we get 49 individual chips out of each wafer, and on each one of those chips there are over 500,000 unique features, and each one of those features has millions of identical DNA probes on them.

5. Spotted Arrays

6. Expression Array Output
Raw summary statistics
Oligonucleotide arrays
Probe set intensity measure
Spotted arrays
Fold change relative to reference sample
Intermediate summary statistics
Fold change relative to baseline
Significance measures
Indicate if the summary statisic is surprisingly large or small.
Scanned images
Typically processed once and stored.

7. Expression data and us Why we love expression The technology is global
Repeatability is not bad
Many diseases have pronounced expression profiles
Why we hate expression
We’re not interested in mRNAs so much as proteins
It’s noisy
The most interesting genes are really noisy.

8. Expression and network analysis
Coloring nodes by expression data
Puts different expression results in context
Suggests overall compound activity

9. In this section, you will learn
Cytoscape’s expression data format
Coloring nodes by expression data
Defining node shape by expression significance data.

10. Checkpoint questions
What are some things that expression data can tell you?
What are some things that expression data cannot tell you?