1. Course Work Project Project title “Data Analysis Methods for Microarray Based Gene Expression Analysis” Sushil Kumar Singh (batch 2002-03) IBAB, Bangalore Done at Siri Technologies Pvt. Ltd. Bangalore

2. Outline Introduction Overview of Data Analysis Normalization Clustering Algorithms Future work Acknowledgements Questions ???

3. Introduction

4. Overview of Data Analysis

5. Normalization An attempt to remove systematic variation from data. Sources of systematic variation – Biological source Influenced by genetic or environmental factors, Age, sex etc. Technical source Induced during extraction, labelling, and hybridization of samples Printing tip problems Measurement source Different DNA conc. Scanner problem

6. Why Normalize Data To recognize the biological information in data. To compare data from one array to another. In practice we do not understand the data – inevitably some biology will be removed too.

7. Normalization methods Methods of elements selections Housekeeping genes All elements Using Spiked control Methods to calculate normalization factor Log ratio Lowess Ratio statistics

8. Clustering For a sample of size “n” described by a d- dimensional feature space, clustering is a procedure that Divides the d-dimensional features in K-disjoint groups in such a way that the data points within each group are more similar to each other than to any other data point in other group.

9. Clustering algorithms Unsupervised – without a priory biological information Agglomerative – Hierarchical Divisive – K-means, SOM Supervised – a priory biological knowledge Support vector machine ( SVM)

10. Hierarchical clustering (HC) Agglomerative technique steps The pair-wise distance is calculated between all genes. The two genes with shortest distance are grouped together to form a cluster. Then two closest cluster are merged together, to form a new cluster. The distances are calculated between this new cluster and all other clusters Steps 2 to 4 are repeated until all the objects are in one cluster.

11. HC contd. Data table

12. HC contd. Calculation of distance matrix using data table. Experiment » Axis Log ratio of genes » Coordinates For n-experiments n dimensional space

13. HC contd. Distance between genes Euclidean distance Pearson correlation Semi-metric distance – Vector angle Metric distance – Manhattan or City block

14. HC contd. Distance between clusters Single linkage clustering Complete linkage clustering Average linkage clustering UPGMA Weighted pair-group average Within-groups clustering Ward’s method

15. HC contd. The result of HC displayed as branching tree diagram called “Dendrogram”. Pros and cons of HC Easy to implement, quick visualization of data set. Ignores negative associations between genes, falls in category of greedy algorithms.

16. K-means Clustering Divisive approach Steps Specify K-initial clusters and find their centroid. For each data point the distance to each centroid is calculated. Each data point is assigned to its nearest centroid. Centroids are shifted to the center of data points assigned to it. Steps 2-4 is iterated until centroid are not shifted anymore.

17. K-means clustering contd. Pros and Cons No dendrogram It is a powerful method if one has prior idea about the no. of cluster, so it works well with PCA.

18. Future Work It includes similar analysis on Self Organizing Map (SOM) Support Vector Machine (SVM) Relevance Network Gene Shaving Self Organizing Tree Analysis (SOTA) Cluster Affinity Search Technique (CAST)

19. Acknowledgements Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore Dr. Ashwini K Heerekar (Siri Technologies Pvt. Ltd, Bangalore) Dr. Jonnlagada Srinivas (Siri Technologies Pvt. Ltd, Bangalore) Mr. Kiran Kumar (Siri Technologies Pvt. Ltd, Bangalore) Mr. Mahantha Swamy MV. (Siri Technologies Pvt. Ltd, Bangalore)

20. Selected references: A Biologist Guide to Analysis of DNA Microarray DATA, by Steen Knudsen DNA Microarrays And Gene Expression from experiment to data analysis and modeling, by P. Baldi and G. Wesely Papers: Computational Analysis of Microarray Data by John Quackenbush, Nature Genetics Review, June 2001, vol2. The use and analysis of Microarray Data by Atul Butte, Nature Review drug discovery, Dec 2002, vol1. Microarray Data Normaliation and Transformation by John Quackenbush, Nature Genetics.

21. Questions ???

22. Thank You