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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
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