Functional Genomics

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Functional Genomics
http//www.ruf.rice.edu/metabol/images/genotype.j
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What is 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.

http//en.wikipedia.org/wiki/Functional_genomics
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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

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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)

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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

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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) _at_ 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/

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For next time

• Read about R
• http//www.r-project.org/
• You might find the following link to Dr. Karl
  Bromans 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.h
  tml
• http//www.reallylinux.com/docs/basic.shtml
• Next timeKeith Hutchison will lecture on
• Genome Structure/Sequence Variation

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