Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.
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Transcript of Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.
![Page 1: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/1.jpg)
Tutorial on Current Biochemical Pathway Visualization Tools
ByRana Khartabil
![Page 2: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/2.jpg)
1. BioCarta
Main focus: Pathways and tools to study them.
Pathway tool is web-based. http://www.biocarta.com/genes/index.asp
Static pages of pathways. Metabolic and regulatory pathways.
Need licence to add/edit pathways.
![Page 3: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/3.jpg)
1.1 BioCarta Homepage
![Page 4: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/4.jpg)
1.2 BioCarta Metabolic Pathway Example Glycolysis. Compounds
shown in chemical and textual form.
Enzymes above arrows with legend at bottom.
Only enzymes are clickable.
![Page 5: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/5.jpg)
1.3 BioCarta Regulatory Pathway Example ATM signalling
pathway. All genes are
clickable.
![Page 6: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/6.jpg)
2. ExPASy “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.
![Page 7: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/7.jpg)
2.1 ExPASy Homepage
![Page 8: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/8.jpg)
2.2 ExPASy Metabolic Pathway Example 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.
![Page 9: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/9.jpg)
2.3 ExPASy Regulatory Pathway Example Insulin receptors. Only enzymes
and arrows outside diagram are clickable.
![Page 10: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/10.jpg)
3. KEGG “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.
Metabolic and Regulatory pathways. Different organisms.
![Page 11: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/11.jpg)
3.1 KEGG Homepage
![Page 12: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/12.jpg)
3.2 KEGG Metabolic Pathway Example
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.
![Page 13: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/13.jpg)
3.3 KEGG Regulatory Pathway Example MAPK signaling
pathway (Homo Sapiens).
![Page 14: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/14.jpg)
4. WIT “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.
![Page 15: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/15.jpg)
4.1 WIT Homepage
![Page 16: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/16.jpg)
4.2 WIT Metabolic Pathway Example Glycolysis
. Enzymes.
Substrates, and products are clickable.
![Page 17: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/17.jpg)
5. MetaCyc 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.
![Page 18: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/18.jpg)
5.1 MetaCyc Software
![Page 19: Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.](https://reader030.fdocuments.net/reader030/viewer/2022032607/56649eca5503460f94bd7e51/html5/thumbnails/19.jpg)
5.2 MetaCyc Metabolic Pathway Example Glycolysis. Everything
(Substrates, products, adjacent pathways, and arrows) is clickable.