1. Analysis of GO annotation at cluster level by Agnieszka S. Juncker

2. Advanced Data Analysis
The DNA Array Analysis Pipeline
Question
Experimental Design
Array design
Probe design
Sample Preparation
Hybridization
Buy Chip/Array
Image analysis
Normalization
Expression Index
Calculation
Comparable
Gene Expression Data
Statistical Analysis
Fit to Model (time series)
GO annotations
Advanced Data Analysis
Clustering PCA Classification Promoter Analysis
Meta analysis Survival analysis Regulatory Network

3. Gene Ontology
Gene Ontology (GO) is a collection of controlled vocabularies describing the biology of a gene product in any organism
There are 3 independent sets of vocabularies, or ontologies:
Molecular Function (MF)
e.g. ”DNA binding” and ”catalytic activity”
Cellular Component (CC)
e.g. ”organelle membrane” and ”cytoskeleton”
Biological Process (BP)
e.g. ”DNA replication” and ”response to stimulus”

4. Gene Ontology structure

5. Cluster analysis and GO
Analysis example:
Partitioning clustering of genes into e.g. 15 clusters based on expression profiles
Assignment of GO terms to genes in clusters
Looking for GO terms overrepresented in clusters

6. Hypergeometric test
The hypergeometric distribution arises from sampling from a fixed population.
10 balls
• We want to calculate the probability for drawing 7 or more white balls out of 10 balls given the distribution of balls in the urn
20 white balls
out of
100 balls

7. Yeast cell cycle Time series experiment: Gene expression profiles: Y
Sampling
Time series
experiment:
Gene expression
profiles:
Time Y
Time
Gene1
Gene2

8. R stuff
Indexing of a matrix (used when you wish to select a subset of your data, e.g. specific rows or columns):
Example 1
rowindex <- 1:10
colindex <- 1:5
datamatrix[rowindex, colindex] # first 10 rows, first 5 columns
datamatrix[1:10, 1:5] # gives the same as above
“Missing” rowindex (or columnindex) means that all rows (or columns) are selected
Example 2
datamatrix[1:5,] # 5 first rows, all columns
datamatrix[,5:10] # all rows, columns 5 to 10
datamatrix[,] # is the same as datamatrix