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A Basic Introduction to Genomics and Proteomics
1. A Basic Introduction
to Genomics
and OpenHelix
John Ben DeVette
johnben@devettepublishing.com
April 2012
1
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2. What is Genomics?
Genomics: the study of all the genes in a cell, or living
organism, including: DNA, RNA, and Protein
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3. a GENOME is
the entire DNA sequence
(chain) and the gene
information for that organism
• Each organism has 1 unique DNA
• DNA orchestrates the manufacture of
genes, protein, and all the life systems of an
organism
• The human genome has 25,000 genes inside
• Like a finger print or eye retina are unique, the
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3
4. All living things are made of protein
The human body has
100,000 proteins
There are
10,000,000 different
proteins building the
world’s organisms
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5. What is the relationship between
proteins, RNA and DNA?
For example,
imagine that a car
is a living organism
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6. DNA is a description
of all the parts of the whole car
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7. RNA reads the description,
and builds the parts
DNA gives
instructions
RNA builds
each part
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8. Each unique car part
is the same as a unique protein
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9. When all the car parts are assembled
then you have a complete car
When all the proteins
are combined you
have a living organism
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10. Together, all the parts
make a car All the proteins
make an organism
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11. Proteomics: is the study of proteins
• Structure: appearance and formation
• Interactions: with other proteins or organisms
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12. Quick review …
What is Genomics?
• Genomics: the study of all the genes in a cell, or
living organism, including:
1. DNA (genotype)
2. RNA (transcriptome)
3. Protein (proteome)
• Proteomics: the study of proteins
– Structure: appearance and formation
– Interactions: with other proteins or organisms
• Bioinformatics: the use of math and computer science
to study biology and especially genomics and
proteomics
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13. The human genome looks like this…
It is shaped like a ball Numerically, it appears like this:
This is BIOINFORMATICS:
using numbers and charts
to represent 3D (real) life
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14. The Project to Map the
Human Genome
• It was a “Race” between
private industry and public
universities
• The project cost $3 billion, and
took 12 yrs
• Finished in 2002.
• Was called “the Golden Path”
• Public universities “won” and
the human genome
information was released on
web, available free / Open
Access.
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15. Speed and Cost of Mapping
• First human genome
took 12 yr and $3 billion
• Today, it takes 3 days
and costs US $10,000
• 2013 will cost $1,000
and take 4 hours
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16. Genomic Explosion
Since 2002, over 3,000 completed genomes
have been mapped.
200+ eukaryotes such as puffer
fish, chicken, dog, fruit
fly, mouse, rat, bee, chimpanzee, cow, flatwor
m, sheep, pig, sea urchin
Corn, rice, grapes, nuts
Bacteria, viruses
Hundreds more are
being completed every year.
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17. We are entering
a new age of discovery:
THE GENOMICS ERA
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18. Genomics will impact almost every field of
study, and will change our lives …
Health & medicine, Biology & Chemistry,
Agriculture, Energy, Defense, Law, Engineering,
Archaeology & Anthropology,
Public Administration & Business,
And new areas of science that we
do not even know about yet!
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19. Genomics and
Energy
Genomists are studying
the fungi genome
to understand which
proteins speed
up, or slow down
combustion (fire)
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20. Spontaneous Combustion
is often caused by fungi
The specific genes are identified and isolated. And then
manufactured and sold to biological-fuel energy
generation companies
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21. Apple Computer’s iCloud server site
in North Carolina, USA
will manufacture renewable energy
from bio-gas
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22. Genomics and
Law
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24. Disease Diagnosis
• Scanning genes for disease risks
• Detecting cancer early
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25. Human gene
analysis to detect
www.23andme.com
disease risk
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27. Pharmaco-genomics:
Drug therapies
tailored to individuals
• Design drug therapy based
on the individual’s genome
• Small differences in each person’s genome
causes different response to drugs
• Protect people who will suffer harmful side
effects from particular drugs
• Future will be custom-designed drugs for each
person, based on their genome map.
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28. The growth in Genomic Resources is huge:
4000+ today
Sequence in data repositories (in
mega bps)
Number of Databases & Resources
in NAR
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29. Zebrafish and human genome
are similar and possess many
homologues (similar genes)
• Zebrafish are easy to breed
• Easy to change Zebrafish genes and test quickly
• Safe way to simulate human genome testing
• Important in cancer research
• Univ of Utah, Huntsman Cancer Inst received
the Nobel Prize in 2002 for colon cancer
research done via Zebrafish.
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30. Chinese and American catfish
genes are used to study
human LIVER CANCER
Because a gene in the liver
of catfish and humans are
similar: homologues.
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31. Challenge: Finding the right resource
• Thousands of resources in dozens of areas
• Variation and Medical
• Protein 00
• Pathways
• Nucleotides
• Literature
• Genome Databases (prokaryotes and viruses)
• Genome Databases (Eukaryotes
• Expression
• Analysis and Algorithms
32. 4000 Databases are too many for
anyone to search
or even learn effectively
OpenHelix focuses on the 300 most important
resources and tools.
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33. Human Genome Project
• The human genome
information was released on
web, available free / Open
Access.
• The information is hosted at
UC Santa Cruz
• Now known as the UCSC
Genome Browser
• Since 2003 UCSC has been
outsourcing to OpenHelix to
do their online training and
seminars
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34. UCSC HOMEPAGE
Since 2003, OpenHelix has developed
and continues to support a set of 6
tutorials for UCSC.
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35. UCSC HOME PAGE LINK TO TRAINING
MATERIALS
LINK TO
UCSC
TRAINING
PAGE
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36. OpenHelix maintains
the top UCSC Tutorial
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37. OpenHelix’s UCSC UCSC outsources to OpenHelix to
BROWSER TUTORIAL
provide online training for the UCSC
Landing page Browser
Genome
Click on this link to launch the actual
tutorial in a new window: UCSC Genome
Browser: An Introduction
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38. NIH awarded
OpenHelix a grant
to develop 100
Online Tutorials for
the world’s top
genomic resources
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39. NIH uses
OpenHelix
Online Tutorials
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40. SciVerse / Science Direct
Example of OpenHelix Application
In 2011, Elsevier SciVerse / ScienceDirect
choose OpenHelixto custom design a
collection of applications for
genomics & bioinformatics
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41. Worldwide
Genomic Databases
OpenHelix has
107 tutorials
for the top 90 resources
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42. Search for Resources:
www.openhelix.com
tag AND snps
tag AND snps Search
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44. Find Resources: www.openhelix.com
Resources
that match
query
Available
tutorials
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45. Search Results: www.openhelix.com
Go to resource
Query match
View movie in OH training
Training Materials
materials
Query match
in OH Blog
Query match
on resource
website
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46. Solution: OpenHelix Training
• 100 Online Tutorial Suites
– Self-run narrated tutorial
• Introduction on how to use the resource
• Chapters for easy navigation
• Use from beginning to end or as reference
– Training Materials
• PowerPoint Slides with suggested script
• Slide Handouts
• Exercises
– Consistent interface and high quality
– One place to learn
47. Training Materials: Tutorial
Tutorial
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48. Training Materials: Slides
Slides
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49. Training Materials: Exercises Exercises
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50. Subscribed Tutorials:
www.openhelix.com/subscriptions.sht
• ml
Tutorials and Training Materials on nearly 100
resources including:
– dbSNP
– NCBI Entrez
– dbGaP
– STRING Tutorials
– Ensembl
– GHR
– GIBBS Motif Sampler
– miRBase
– PFAM & many more…
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51. Sponsored Tutorials:
www.openhelix.com/cgi/freeTutorials.
• cgi
Sponsored Resource Tutorials
– PDB
– UCSC Genome
– UCSC Table Browser
– UCSC Additional
Tools Sponsored Tutorials
– SBKB
– ENCODE
– NIEHS SNPs
– World Tour
– And more…
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52. OpenHelix Blog: blog.openhelix.com
• Daily news and information
about genomics
data, research and resources
• Weekly video tips on how to
use database and tool
features
• Weekly “What’s the Answer”
thread of biological resource
questions and answers from
BioStar
• More…
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53. Additional Progrms
• BioMed Central
– Articles are searched for resources
– We show the resources that we have tutorials on
– User can click on resource name to go to the tutorial
• Elsevier’s ScienceDirect
– Same as BMC, except as part of the Elsevier third
party application program
– Users choose to add the plug-in to their ScienceDirect
platform
• SciVee (www.scivee.tv)
– OpenHelix “channel” to watch tip of the weeks
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54. OpenHelix Customers
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55. Subscription benefits
• Researchers use tutorials to learn new
genomics databases and resources
• Professors save time in creating classroom
content
• All use tutorials to keep abreast of new
resources
56. Subscription benefits
• Onsite training limits who can attend
• View anywhere, anytime
• Available “at your fingertips” when
researching articles in BioMed Central and
Elsevier SciDirect
58. Subscription benefits
• Some companies and institutions have
dedicated bioinformatics' employees or
“cores”
• OpenHelix subscriptions give them the time to
focus on more critical tasks—leave
introductory training to us
• 10,000s of hours creating and updating
tutorial suites
– Not cost effective to reproduce
59. Subscription benefits
• Been training on bioinformatics resources
since 2003
• Extensive relationships with resource
providers
• Relied on by many resource providers to
create their training programs
60.
61. Current resource providers
• UCSC Genome Browser
– University of California, Santa Cruz
– Funded by National Human Genome Research
Institute
• ENCODE
– University of California, Santa Cruz
• Protein Data Bank
– Rutgers and University of California, San Diego
– Multiple funders
• Structural Biology Knowledge Base
62.
63. End Users (Subscribers)
• Government Agencies
– National Institutes of Health
• Research Centers
– MD Anderson Cancer Center
– Children’s Mercy Hospital
• Medical Colleges
– Mt. Sinai School of Medicine
• Universities
– Vanderbilt
– Washington University
• Biotech/Pharma
– SRC Inc.
64. Worldwide
Genomic Resource
Training and Support
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Editor's Notes
The keyword cloud is known as a Wordle.
Since there are 7 billion people in the world today, there are 7 billion different human genomes.
As of 2007, we have identified 1m< unique proteins from about 100 organisms
You may want to tell the audience, A car has 30,000 parts
Each part of a car is like each protein of a human bodyRNA makes each part and assembles them into a car.
The definition of BIOINFORMATICS is rigged to enter slowly. Make sure to wait for it.
The shape is real, but colors are added for effect.The numerical sequence on the right is only a small portion of an entire genome
NEW MACHINE $50,000WILL BECOME A COMMON TOOL TO ANALYZE GENOME, EVERYONE CAN DO IT.IT WILL BE AVAILABLE ALL AROUND THE WORLD
Most commonly studied fungi are shelf mushrooms Thermophilic (cause combustion) and thermotolerant (inhibit combustion)
Hay stacks burning in USA
This server storage site is opening in 2012Renewable energy means the energy does not come from fossil fuels like coal or oil.Increasingly, more and more energy will be created from burning animal waste or recycling garbage and turning it into “bio-gas”.Genome research is playing a crucial role in the development of bio-fuels.
Already there are hundreds of criminal and patent legal battles where a genome is critical evidence. In 2013 when the cost of mapping and identifying a genome drops to $1,000 the number of cases will probably increase 1000%
$100
A homologue is when the gene of two different species is almost the same.
UCSC: University of California at Santa CruzThis is the UCSC Genome and Bioinformatics home pageThe UCSC Browser is the most popular and commonly used resource to study genomics in the world. It is free.[march 2012]