Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Pathways, Metabolites and Disease

Maciej Lalowski

Biomedicum Helsinki,Helsinki University

Trasmed course 02.11.2010

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Hierarchical Clustering

Basics

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Hierarchical ClusteringWe have a number of datapoints in an n-dimensional space, and want to evaluate which data points clustertogether.

This can be done with a hierarchicalclustering approach

It is done as follows:

1) Find the two elements with thesmallest distance (that means themost similar elements)

2)These two elements will be clusteredtogether. The cluster becomes a newelement

3)Repeat until all elements areclustered

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Important parameters in hierarchical clustering are:

The distance methodThis measure defines how the distance between two datapoints is measuredin generalAvailable options: Euclidean (default), Minkowski, Cosine, Correlation,Chebychev, Spearman

The linkage methodThis defines how the distance between two clusters is measuredAvailable options: Average (default) and Ward

Use PCA data:Determines if the data is pretreated with a PCA.Only reasonable if used withEuclidean metrics and with a reduction of explained variance

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Entrez Gene: http://www.ncbi.nlm.nih.gov/gene/:

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Entrez Gene: http://www.ncbi.nlm.nih.gov/gene/:

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Entrez Gene: http://www.ncbi.nlm.nih.gov/gene/:

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

AmiGO: http://amigo.geneontology.org/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Gene Ontology annotation: http://www.ebi.ac.uk/GOA/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Gene Cards: http://www.genecards.org/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Gene Cards: http://www.genecards.org/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Gene Cards: http://www.genecards.org/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

Gene Cards: http://www.genecards.org/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

KEGG http://www.genome.jp/kegg/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

KEGG http://www.genome.jp/kegg/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

KEGG http://www.genome.jp/kegg/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

KEGG http://www.genome.jp/kegg/

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

REACTOME

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

REACTOME

Protein Chemistry/Proteomics/Mass spectrometry Uni. of Helsinki

OMIM