Tutorial on Current Biochemical Pathway Visualization Tools

ByRana Khartabil

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.

1.1 BioCarta Homepage

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.

1.3 BioCarta Regulatory Pathway Example ATM signalling

pathway. All genes are

clickable.

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.

2.1 ExPASy Homepage

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.

2.3 ExPASy Regulatory Pathway Example Insulin receptors. Only enzymes

and arrows outside diagram are clickable.

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.

3.1 KEGG Homepage

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.

3.3 KEGG Regulatory Pathway Example MAPK signaling

pathway (Homo Sapiens).

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.

4.1 WIT Homepage

4.2 WIT Metabolic Pathway Example Glycolysis

. Enzymes.

Substrates, and products are clickable.

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.

5.1 MetaCyc Software

5.2 MetaCyc Metabolic Pathway Example Glycolysis. Everything

(Substrates, products, adjacent pathways, and arrows) is clickable.