Microarray GEO – Microarray sets database

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Presentation transcript:

Microarray GEO – Microarray sets database EPClust – Microarray data analysis

Microarray Data Matrix Input Methods Unsupervised Clustering Hierarchical clustering Partition methods

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.

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

Microarray Data Matrix

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

Microarray Data: Clusters

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

How to determine the similarity between two genes?

How to determine the similarity between two clusters?

How to determine the similarity between two clusters?

How to determine the similarity between two clusters?

Hierarchical clustering result

Microarray Data: Clustering K-mean clustering is an algorithm to classify The data into K number of groups. http://home.dei.polimi.it/matteucc/Clustering/tutorial_html/AppletKM.html

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

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

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 http://www.ncbi.nlm.nih.gov/geo/

Platform: Affymetrix GeneChip Human Genome Samples: 11 psoriasis patients

Download dataset Clustering Statistic analysis

Searching for expression profiles in the Human Genome browser.

Keratine 10 is highly expressed in skin

Transpose,Normalize,Randomize

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

Initial seeds Final seeds 10 clusters