1. Functional Genomics Carol Bult, Ph.D. Course coordinator carol.bult@jax.org The Jackson Laboratory Winter/Spring 2012 Keith Hutchison, Ph.D. Course co-coordinator keithh@maine.edu University of Maine http://www.ruf.rice.edu/~metabol/images/genotype.jpg

2. What is Functional Genomics? http://en.wikipedia.org/wiki/Functional_genomics A field of molecular genetics that uses genome-wide, high-throughput measurement technologies to understanding the relationships between genotype and phenotype –Genomics, epigenomics, transcriptomics, proteomics –Computational genomics (data mining) –Transgenics, targeted mutations, etc.

3. What topics will this course cover? Primary focus: –Transcriptional profiling using microarrays and high-throughput sequencing (RNA-Seq) – Data analysis R statistical programming language/environment Galaxy sequence analysis workflow system Other topics: –Genome structure and sequence variation –Epigenomics –Bio-ontologies –Proteomics –Metabolomics

4. How will this course be structured? Lectures and readings assigned by instructors Assignments and discussion (50% of grade) Student project (50% of grade) –Choose a data set to analyze from several options –Do some background research on the data set –Perform an analysis of the data –Write up the analysis in the format of a scientific manuscript as if you were submitting the manuscript to PLOS Computational Biology http://www.ploscompbiol.org/home.action –Oral presentation on the project Preliminary results mid-course (15 minutes per student) Final presentation at end of course (20 minutes per student)

5. Who are the instructors? Carol Bult (JAX), course coordinator –Microarrays, Using R, Galaxy Keith Hutchison (UM), co-coordinator –Genome structure/variation Gary Churchill (JAX) –experimental design Doug Hinerfeld (JAX) –next generation sequencing and proteomics Judith Blake (JAX) –bio-ontologies Matt Hibbs (JAX) –mining expression data Joel Graber (JAX) –RNA processing

6. What resources will be used for this course? Class Web Site –functionalgenomics.wordpress.com R Project for Statistical Computing –http://www.r-project.org/ Gene Expression Omnibus (GEO) @ NCBI –http://www.ncbi.nlm.nih.gov/geo/ Gene Ontology web site –http://www.geneontology.org/http://www.geneontology.org/ Maine Innovation Cloud –http://www.cloud.target.maine.edu/

7. For next time Read about R –http://www.r-project.org/http://www.r-project.org/ –You might find the following link to Dr. Karl Broman’s into to R useful: http://www.biostat.wisc.edu/~kbroman/Rintro/ In the next week you will be given an account on the Maine Innovation Cloud which will give you access to R –You will need some basic Linux/Unix commands to use the Cloud http://code.google.com/edu/tools101/linux/basics.html http://www.reallylinux.com/docs/basic.shtml Next time…Keith Hutchison will lecture on –Genome Structure/Sequence Variation