Transcript Why teach a course in bioinformatics?

Arrays:
• Narrower terms include bead arrays, bead based
arrays, bioarrays, bioelectronic arrays, cDNA arrays,
cell arrays, DNA arrays, gene arrays, gene
expression arrays, genome arrays, high density
oligonucleotide arrays, hybridization
arrays, microelectronic arrays, multiplex DNA
hybridization arrays, nanoarrays, oligonucleotide
arrays, oligosaccharide arrays, protein arrays,
solution arrays, spotted arrays, tissue arrays, exon
arrays, filter arrays, macroarrays, small molecule
microarrays, suspension arrays, tiling arrays,
transcript arrays. Related terms include arrayed
library. See also chips, microarrays.
Microarray Technology?
What is it??
The future . . .
• DNA microarrays (also
called DNA chips or Gene
chips) are miniaturized
laboratories for the study of
gene expression.
• Microarrays are small pieces of
glass (or silicon or nylon) about 2
or 3 cm square, coated with DNA.
• The DNA is spotted by high speed
robots in a very precise pattern.
The droplets of DNA (measured in
pL or nL) are separated by _x_
microns.
• The surface of the array is covered
with thousands, tens of thousands, (or
soon with hundreds of thousands) of
spots, each spot containing a different
DNA oligomer.
• Each oligomer in a DNA microarray
can serve as a probe to detect a
unique, complementary DNA or RNA
molecule.
Many microarray experiments
have been performed with Yeast.
• Why?
• Genome is completely sequenced and
well annotated.
• Select a PCR primer pair that amplifies
each ORF.
PCR primers for sale . . .
• To our sales list we add Yeast ORF
specific primers for over 6,000 ORFs!
These primers have been designed to
amplify, from genomic DNA, the
complete coding region including the
start and stop codons. For yeast this is
possible as very few yeast genes
contain introns.
• GCAT Animation
See CSUS Microarray Data
• - Finding GCAT Data on SMD
• DNA Microarray Technique (animatedrequires Flash plug-in)
There are two distinct way of
making DNA arrays:
• DNA microarrays: Also referred to as
"microarrays." Non- porous solid supports,
such as glass have facilitated miniaturization
and fluorescence based detection. About
10,000 cDNAs can be robotically spotted onto
a microscope slide and hybridized with a
double labeled probe, using protocols
pioneered by Pat Brown and colleagues at
Gene Chips or DNA Chips
• Oligomers synthesized directly on the chips
(pioneered by Affymetrix). GeneChip ® is an
Affymetrix product where they have adapted
photolithographic masking techniques used in
semiconductor manufacture to produce arrays with
400,000 distinct oligonucleotides.
How to build a Gene Chip
• Add nucleotides one by one to the growing end of
an oligonucleotide, the sequence determined by the
order in which the dNTPs are added to the reaction
mix.  ?
• Modified dNTPs are added. dNTPs can not attach
to another until they are light activated. The dNTPs
are added one after another to the chip surface, and
photolithography is used to direct pulses of light at
individual positions in the array and determine
which of the growing oligonucleotides will be
extended by one unit.
Affymetrix –
• DNA is short (25 nt)
• Small variances (SNPs) can be detected
• Only one Dye can be used at a time
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DNA Microarrays
cDNA is spotted on glass plates
cDNA is from 100nt to 2kb in length
Very efficient hybridization
Small variances (SNPs) can’t be seen
#1 use of Microarrays- Investigate
Changes in Gene Expression.
Compare cells before and after perturbation:
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Nutritional
Environmental
Disease
Toxin
Different Stages of Development
Important ??
• This opens the possibility of
identifying patterns of coregulation
among genes, which, in turn,
reflects underlying regulatory
mechanisms and function
interrelationships.
Microarrays are the Future of Biology
• Pre-Genomic Era- Study of Individual Genes using
techniques of Molecular Biology.
• Genomic Era- Sequencing of entire genomes.
Analytical techniques include Sequencing, Gene
Finding, analysis of Sequence Homology
• Post-Genomic Era- Analysis of Gene Expression.
Techniques include microarray, functional
annotation techniques.
Researchers love DNA chips;
Doctors will soon love DNA chips
• Researchers love DNA chips because they
give a huge amount of information, fast, at
low cost.
• Doctors will soon learn to love them because
there are many times when a doctor would
like to know something about a patient's
genes (such as whether the patient is likely
to respond well to a certain drug). When the
price comes down enough, microarrays will
likely become routine tools in the doctor's
office.
Clinical Applications?
• If this research pays off, scientists and
doctors will see a new, more
informative face of cancer for individual
tumors. That could produce tremendous
gains in cancer care.
• Doctors could better match patients to
the best treatment. That could improve
the outcome and spare patients the side
effects of therapies that won't help.
• PNAS -- article
Why microarrays in a
bioinformatics class?
• Design of chips
• Quantitation of signals
• Extraction of groups of genes with
linked expression profiles.
• Since the development of DNA
microarray technology in the
late 1990s, it has become
apparent that the increase in
available gene expression data
will eventually parallel the
growth of the sequence and
structure databases.
2 important topics requiring
computers:
Data Integration
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It’s important to link the data from the array
experiment with other sequence databases
(Genbank, SwissProt, etc).
If the activity of a gene has changed, you want
to be able to view pre-existing information about
the gene in order to explain the experimental
results.
To exchange array data with other researchers,
you need some standardized format.
Gene Clustering
Group together genes with similar patterns of
expression:
Clustering can be thought of as forming a
phylogenetic tree of genes or tissues. Genes are
near each other on the "gene tree" if they show a
strong correlation across experiments, and tissues
are near each other on the "tissue tree" if they have
similar gene expression patterns.
• PNAS -- Alon et al. 96 (12): 6745
• Pattern searching and gene clustering of
promoter regions of Drosophila olfactory
receptors
The End