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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
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


What is sorting

Time

Height

What is sorting?

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



Distance matrices
Distance matrices

samples distance matrix

samples

Genes distance matrix

genes

genes

Expression matrix

genes

samples



Multiple clusters

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
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 on a circle

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.


Electronic microdissection

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 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
Software availability

  • SPIN is available upon request.

  • Email [email protected]




The excel1
The EXCEL

Shift header line one column to the left


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