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Tutorial on Current Biochemical Pathway Visualization Tools

Tutorial on Current Biochemical Pathway Visualization Tools. By Rana 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.

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Tutorial on Current Biochemical Pathway Visualization Tools

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  1. Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil

  2. 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.

  3. 1.1 BioCarta Homepage

  4. 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.

  5. 1.3 BioCarta Regulatory Pathway Example • ATM signalling pathway. • All genes are clickable.

  6. 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.

  7. 2.1 ExPASy Homepage

  8. 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.

  9. 2.3 ExPASy Regulatory Pathway Example • Insulin receptors. • Only enzymes and arrows outside diagram are clickable.

  10. 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.

  11. 3.1 KEGG Homepage

  12. 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.

  13. 3.3 KEGG Regulatory Pathway Example • MAPK signaling pathway (Homo Sapiens).

  14. 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.

  15. 4.1 WIT Homepage

  16. 4.2 WIT Metabolic Pathway Example • Glycolysis. • Enzymes. Substrates, and products are clickable.

  17. 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.

  18. 5.1 MetaCyc Software

  19. 5.2 MetaCyc Metabolic Pathway Example • Glycolysis. • Everything (Substrates, products, adjacent pathways, and arrows) is clickable.

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