Transcript w0405_tutorial13

Introduction to Bioinformatics Tutorial no. 13
Probe Design
Gene Networks
Probe design problem
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Given a genome with a set of genes.
Recall that each gene is represented by a
probe (a short segment) of the corresponding
cDNA.
The length of a probe can be 20, 50, 70!
The probe design problem tries to identify a
probe for every gene.
Probe design problem
(Informal definition)
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X2
X3
X4
p1
Xp1
Xp1
Xp1
Given a genome, for every cDNA (or mRNA) Xi,
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a probe pi is identified such that
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X1
pi is a substring of Xi; and
pi does not cross-hybridize with other mRNAs
Probe design problem creates a probe pi for
every mRNA Xi
Primer3 Input
Repeats
library
Sequence
5’ PCR
primer
Oligo
probe
3’ PCR
primer
Exclude from
PCR primer
Include in
PCR primer
Primer3 Output
Product
Length
mRNA position
% GC
Self complementarity
Hybrid Tm
Sequence
3’ complementarity
5’ PCR
primer
Oligo
probe
3’ PCR
primer
OligoDB
Sequence name to find
OligoDB Input
Oligonucleotide length
Number for
each mRNA
Background database
Ensembl
mRNA ID
Ensembl
Gene ID
OligoDB Output
mRNA
position
Tm of
hybrid
Probe
stability
Background
matches
Oligo
probe
Biochemical Pathway Visualization Tools
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BioCarta
EXPASY
KEGG
WIT
MetaCyc
BioCarta
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Main focus: Pathways and tools to study
them.
Pathway tool is web-based.
http://www.biocarta.com/genes/index.asp
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Static pages of pathways.
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Metabolic and regulatory pathways.
Need licence to add/edit pathways.
BioCarta Homepage
BioCarta Metabolic Pathway Example
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Glycolysis.
Compounds shown in
chemical and textual
form.
Enzymes above arrows
with legend at bottom.
Only enzymes are
clickable.
BioCarta Regulatory Pathway Example
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ATM signalling
pathway.
All genes are clickable.
ExPASy
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“Expert Protein Analysis System”.
Main focus: Analysis of protein sequences and
structures.
Pathway tool is web-based.
http://www.expasy.org/cgi-bin/search-biochem-index
Static pages of pathways.
 Metabolic and Regulatory pathways.
 Scanned in version of the Boehringer Mannheim
“Biochemical Pathways” map.
 Map partitioned into 115 pieces.
 Keywords matched against entries in map.
Cannot add/edit pathways.
ExPASy Homepage
ExPASy Metabolic Pathway Example
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Glycolysis.
Color convention based on
Michal’s “Biochemical
Pathways”.
 Color of compounds
depends on compound type.
 Color of arrows depend on
species (plant, animal,
yeast, prokaryotes).
Only enzymes and arrows
outside diagram are clickable.
ExPASy Regulatory Pathway Example
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Insulin receptors.
Only enzymes and
arrows outside diagram
are clickable.
KEGG
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“Kyoto Encyclopedia of Genes and Genomes”.
Main focus: Biochemical pathway visualization.
Pathway tool is web-based.
http://www.kegg.com/kegg/kegg2.html
Static pages of pathways.
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Metabolic and Regulatory pathways.
Different organisms.
KEGG Homepage
KEGG Metabolic Pathway Example
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Glycolysis.
Substrates and products
are drawn in circles.
Enzymes, represented by
EC number, are drawn in
rectangles.
Adjacent pathways are
drawn in semi-rectangles.
Enzymes found in the
gene catalog of a specific
organism are marked
green.
All items are clickable.
KEGG Metabolic Pathway Example
Select specific species
Link to
compound
Link to other
pathway
Link to
enzyme
KEGG Regulatory Pathway Example
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MAPK signaling
pathway (Homo
Sapiens).
WIT
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“What is There”.
Main focus: Produce metabolic
reconstructions for sequenced (or partially
sequenced) genomes.
Pathway tool is Web-based.
http://wit.mcs.anl.gov/WIT2/
Static pages of pathways.
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Only metabolic pathways.
WIT Homepage
WIT Metabolic Pathway Example
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Glycolysis.
Enzymes.
Substrates,
and products
are clickable.
MetaCyc
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Electronic encyclopedia of over 450 metabolic
pathways from over 150 different organisms.
Software:
 Implemented in COMMON LISP; AI techniques
incorporated to allow inference, such as pathway
prediction from sequenced genomes.
 Need a licence to obtain software.
 Free for academic purposes only.
Graph layout algorithm for drawing metabolic pathways
dynamically at run-time.
Need to manipulate database to add/edit pathways.
MetaCyc Software
MetaCyc Metabolic Pathway Example
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Glycolysis.
Everything
(Substrates,
products,
adjacent
pathways,
and arrows)
is clickable.
Question
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Do the enzymes form the same pathway share
a common regulation?
Inspect Lysine Biosynthesis pathway.
Use the following tools:
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KEGG: http://www.genome.jp/kegg/
UCSC Genome Browser: genome.ucsc.edu
TransFac database or alternative search tools like
TESS: http://www.cbil.upenn.edu/tess/