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Tutorial on Current Biochemical Pathway Visualization Tools

This tutorial is a detailed guide on utilizing current biochemical pathway visualization tools such as BioCarta, ExPASy, KEGG, WIT, and MetaCyc. It covers key features, examples, and functionalities of each tool, focusing on metabolic and regulatory pathways. Learn how to navigate these web-based tools to study and analyze pathways effectively. Gain insights into pathway visualization, enzyme interactions, and pathway predictions using AI techniques. Discover the importance of these tools in bioinformatics research and academic settings.

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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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