Transcript Tutorial on existing pathway tools

Tutorial on Current Biochemical
Pathway Visualization Tools
By
Rana Khartabil
1. 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.
1.1 BioCarta Homepage
1.2 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.
1.3 BioCarta Regulatory
Pathway Example
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ATM signalling
pathway.
All genes are
clickable.
2. 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.
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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.
2.1 ExPASy Homepage
2.2 ExPASy Metabolic Pathway
Example
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Glycolysis.
Color convention based
on Michal’s “Biochemical
Pathways”.
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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.
2.3 ExPASy Regulatory
Pathway Example
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Insulin receptors.
Only enzymes and
arrows outside
diagram are
clickable.
3. 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.
3.1 KEGG Homepage
3.2 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 semirectangles.
Enzymes found in the
gene catalog of a specific
organism are marked
green.
All items are clickable.
3.3 KEGG Regulatory Pathway
Example
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MAPK signaling
pathway (Homo
Sapiens).
4. 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.

Only metabolic pathways.
4.1 WIT Homepage
4.2 WIT Metabolic Pathway
Example
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Glycolysis.
Enzymes.
Substrates,
and
products
are
clickable.
5. MetaCyc
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Electronic encyclopedia of over 450 metabolic
pathways from over 150 different organisms.
Software:
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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.
5.1 MetaCyc Software
5.2 MetaCyc Metabolic
Pathway Example
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Glycolysis.
Everything
(Substrates
, products,
adjacent
pathways,
and
arrows) is
clickable.