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

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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  1. 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

  2. SPIN • A new method for mining gene expression data • The philosophy behind SPIN – feel and play with the data

  3. Time Height What is sorting? One dimensional ordering of a set of objects according to a particular trait.

  4. Samples distance matrix

  5. Distance matrices samples distance matrix samples Genes distance matrix genes genes Expression matrix genes samples

  6. High Distance Low

  7. Unsorted SPIN Large Small Distances Multiple clusters Q: How many objects? Q: What are their shapes? Q: What is the relative orientation ?

  8. Decode this matrix Q: How many objects? Q: What are their shapes? Q: What is the relative orientation ?

  9. Expression matrix PCA Analysis Distance matrix Cluster buttons Scores & Diagnostics SPC Dendrogram Transpose Sorting buttons SPIN Interface Layout

  10. 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.

  11. 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

  12. Adenomas Liver metastasis Normal Liver Normal colon Lung metastasis Normal Lung Carcinomas

  13. 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.

  14. Software availability • SPIN is available upon request. • Email assif.yitzhaky@weizmann.ac.il

  15. Exercise Time

  16. The EXCEL

  17. The EXCEL Shift header line one column to the left

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