Functional Genomics

Carol Bult, Ph.D.Course coordinatorcarol.bult@jax.org

The Jackson Laboratory

Winter/Spring 2012Keith Hutchison, Ph.D.Course co-coordinator

keithh@maine.eduUniversity of Maine

http://www.ruf.rice.edu/~metabol/images/genotype.jpg

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.

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

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)

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

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/

• Maine Innovation Cloud– http://www.cloud.target.maine.edu/

For next time

• Read about R– 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