1. Microarray GEO – Microarray sets database
EPClust – Microarray data analysis

2. Microarray Data Matrix
Input
Methods
Unsupervised Clustering
Hierarchical clustering
Partition methods

3. Microarray Data Matrix
Each column represents all the gene expression levels from a single experiment.
Each row represents the expression of a gene across all experiments.

4. Microarray Data Matrix
Each element is a log ratio: log2 (T/R), where T is the gene expression level in the testing sample, R is the gene expression level in the reference sample

5. Microarray Data Matrix

6. Different representations
Microarray Data:
Different representations
Log ratio
Log ratio
Exp
Exp

7. Microarray Data:
Clusters

8. Microarray Data: Clustering
Hierarchical Clustering :genes with similar expression patterns are grouped together and are connected by a series of branches (dendrogram).

9. How to determine the similarity between two genes?

10. How to determine the similarity between two clusters?

11. How to determine the similarity between two clusters?

12. How to determine the similarity between two clusters?

13. Hierarchical clustering result

14. Microarray Data: Clustering
K-mean clustering is an algorithm to classify
The data into K number of groups.

15. Microarray Data: Clustering
K-mean clustering is an algorithm to classify
The data into K number of groups.

16. Microarray Data: Clustering
K-mean clustering is an algorithm to classify
The data into K number of groups.

17. Expression profiles by gene
Like Series,but further curated and suitable for analysis with GEO tools
Expression profiles by gene
Probe sets
*further curated= statistically comparable datasets
Microarray experiments
Groups of related microarray experiments

18. Platform: Affymetrix
GeneChip Human Genome
Samples: 11 psoriasis patients

19. Download dataset
Clustering
Statistic analysis

21. Searching for expression profiles in the Human Genome browser.

22. Keratine 10 is highly expressed in skin

28. Transpose,Normalize,Randomize

29. Samples found in cluster
Graphical representation of the cluster
Graphical representation of the cluster

30. Initial seeds
Final seeds
10 clusters