Clustering Algorithms in Bioinformatics: Application to Microarrays and Medicine - Prof. D, Study notes of Bioinformatics

Download Clustering Algorithms in Bioinformatics: Application to Microarrays and Medicine - Prof. D and more Study notes Bioinformatics in PDF only on Docsity! #25 - Clustering Algorithms & Microarrays & Medicine 10/23/06 BCB 444/544 Fall 06 Dobbs 1 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 1 BCB 444/544 - Introduction to Bioinformatics Lecture 26 Microarrays & Medicine #26_Oct23 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 2 Seminars in Bioinformatics/Genomics Mon Oct 23 • Heike Hofmann (Stat) Visualizing Conditional Distributions Statistics Seminar 4:10 PM in 319 Snedecor • Clark Ford (FSHN) Genetic Analysis of QPM Modifiers to Enhance Maize Protein Nutrition Genetics Seminar 12:10 PM in 101A Ind Ed II Thurs Oct 26 • Peter Flynn (Chem, Utah) A New Biophysical Paradigm for Encapsulation Studies BBMB Seminar 4:10 PM in 1414 MBB Fri Oct 27 • Diane Bassham (GDCB) Signal perception, transduction and autophagy in development and survival under stress GDCB Seminar 4:10 PM in 1414 MBB 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 3 Assignments: Reading This Week • Machine Learning Overview & Algorithms • Chp 7: Applied Research with Microarrays Mon Oct 23 GEPAS - Clustering Tutorial (online) Chp 7.2 - Improving Health Care with DNA Microarrays Wed Oct 25 Machine Learning - more Algorithms (Michael) Thurs Oct 26 Lab: Study Guide Review & EXAM 2 - Lab Practical Exam (30 pts) Fri Oct 27 EXAM 2 - In Class Exam (70 pts) 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 4 Assignments & Events: BCB 444 & 544: HW#4: Due at Noon, Mon Oct 23 Exam 2: Thurs Oct 26 - Lab Practical = 30% Fri Oct 27 - In Class Exam = 70% BCB 544 Only: Teams & Projects Any questions? 544Extra#2 Due Mon Nov 6 See updated Schedule (Oct 23) posted online 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 5 Chp 6: Basic Research with DNA Microarrays Chp 6 - Campbell & Heyer Companion Website Copyright © 2006 A. Malcolm Campbell 6.1 Introduction to Microarrays Math Minute 6.1 Why Should You Log-Transform Microarray Data? Math Minute 6.2 How Do You Measure Similarity between Expression Patterns? Math Minute 6.3 How Do You Cluster Genes? 6.2 Alternative Uses of DNA Microarrays Math Minute 6.4 Is It Useful to Compare the Columns of a Gene Expression Matrix? ･ Which Predicted Genes Are Real and Which Ones Aren't? ･ Can Microarrays Improve Annotations? ･ Could a Microarray Validate Annotation of an Entire Genome 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 6 Chp 7: Applied Research with DNA Microarrays Chp 7 - Campbell & Heyer Companion Website 7.1 Cancer and Genomic Microarrays ･ Are There Better Ways to Diagnose Cancer? Math Minute 7.1 What Are Signature Genes & How Do You Use Them? ･ Can Breast Cancer Be Categorized with Microarrays? ･ What Genomic Changes Occur in Cancer Cells? 7.17.2 Improving Health Care with DNA Microarrays ･ Why Is the Tuberculosis Vaccine Less Effective Now? ･ Can We Choose the Most Effective Medication for Each Cancer? ･ Can We Predict Effectiveness of Chemotherapy? ･ What Happens When You Accumulate Fat? ･ What Effect Does Leptin Have on wt Adipose Tissue? Copyright © 2006 A. Malcolm Campbell #25 - Clustering Algorithms & Microarrays & Medicine 10/23/06 BCB 444/544 Fall 06 Dobbs 2 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 7 V Honavar 2006 B Olson 2005 For Microarray Analysis: Primarily clustering & classification algorithms We won't discuss: Experimental design Preprocessing data Normalization & background issues We will discuss: Clustering algorithms (used in lab) Specific applications, interpretation & significance 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 8 GEPAS Documentation: http://gepas.bioinfo.cipf.es/cgi-bin/documentation 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 9 GEPAS Tutorial on Clustering: http://gepas.bioinfo.cipf.es/cgibin/tutoX?c=clustering/clustering.config http://bioinfo.cipf.es/docus/courses/clustering/clustering_tutorial.pdf 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 10 Table MM6.2 Correlation coefficients for each pair of genes (from Table MM6.1) Copyright © 2006 A. Malcolm Campbell Hierarchical clustering algorithm: Which genes would be clustered first? i.e.,Which 2 genes have most similar expression pattern, based on CC? 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 11 Table MM6.4 Summary of hierarchical clustering of 12 genes in Table MM6.2 Copyright © 2006 A. Malcolm Campbell 10/23/06BCB 444/544 F06 ISU Dobbs #25 - Clustering Algorithms & Microarrays & Medicine 12 Fig MM6.1 Dendrogram of clustered genes from Table MM6.3 and Fig 6.8 Copyright © 2006 A. Malcolm Campbell