Spin s orting p oints i nto n eighborhoods algorithm
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SPIN ( S orting P oints I nto N eighborhoods) Algorithm. ELTEM Neurogenomics Course Biozentrum – Basel December 1, 2006 Presented by Tal Shay and Assif Yitzhaky Weizmann Institute of Science Rehovot, Israel.

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SPIN ( S orting P oints I nto N eighborhoods) Algorithm

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SPIN (Sorting Points Into Neighborhoods) Algorithm

ELTEM Neurogenomics Course

Biozentrum – Basel

December 1, 2006

Presented by Tal Shay and Assif Yitzhaky

Weizmann Institute of Science

Rehovot, Israel

D. Tsafrir , I. Tsafrir , L. Ein-Dor , O. Zuk , D.A. Notterman , and E. Domany Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices. Bioinformatics 2005 21: 2301-2308


SPIN

  • A new method for mining gene expression data

  • The philosophy behind SPIN – feel and play with the data


Time

Height

What is sorting?

One dimensional ordering of a set of objects according to a particular trait.


Samples distance matrix


Distance matrices

samples distance matrix

samples

Genes distance matrix

genes

genes

Expression matrix

genes

samples


High Distance

Low


Unsorted

SPIN

Large

Small Distances

Multiple clusters

Q: How many objects?

Q: What are their shapes?

Q: What is the relative orientation ?


Decode this matrix

Q: How many objects?

Q: What are their shapes?

Q: What is the relative orientation ?


Expression

matrix

PCA

Analysis

Distance matrix

Cluster

buttons

Scores &

Diagnostics

SPC

Dendrogram

Transpose

Sorting buttons

SPIN Interface Layout


Side to side

Neighborhood

Side-To-Side on a circle:

Penalizes blue points far from the main diagonal.

Penalizes red points near the main diagonal.


Normal

Liver

Primary

Tumor

Liver Met.

Identify ‘clean’ metastasis samples

‘Electronic Microdissection’

Two-Way Sorted Expression Matrix

Important: 97% of genes that appear significantly over-expressed in Metastasis vs. Carcinoma are Liver-Specific and irrelevant to cancer!

Genes

Normal

Liver

Liver

Met.

Primary

Tumor

Polyp

Normal

Colon


Adenomas

Liver metastasis

Normal Liver

Normal colon

Lung metastasis

Normal Lung

Carcinomas


SPIN versus clustering

  • SPIN rearranges points in a way that reflects the shape of their arrangement.

  • Clustering aims to rearranges points to categories; points within a cluster are more “similar” as compared to points outside the cluster.

  • SPIN rearranges the points and the user should identify the clusters. Clustering do it for you in a formal way.


Software availability

  • SPIN is available upon request.

  • Email [email protected]


Exercise Time


The EXCEL


The EXCEL

Shift header line one column to the left


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