Kyoto Encyclopedia of Genes and Genomes (KEGG)

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1 NPTEL Biotechnology -Systems Biology Kyoto Encyclopedia of Genes and Genomes (KEGG) Dr. M. Vijayalakshmi School of Chemical and Biotechnology SASTRA University Joint Initiative of IITs and IISc Funded by MHRD Page 1 of 14

2 NPTEL Biotechnology -Systems Biology Table of contents 1 INTRODUCTION SYSTEMS INFORMATION GENOMIC INFORMATION CHEMICAL INFORMATION KEGG PATHWAY KEGG LIGAND KEGG BRITE/KEGG GENES/KEGG ENZYME... 9 Joint Initiative of IITs and IISc Funded by MHRD Page 2 of 14

3 1 Introduction After a tedious journey of reading, now let us begin to work and understand how pathways can be mapped, how one can design cell models and networks. KEGG is a very popular resource for pathway mapping and for decoding gene functions from a genomic perspective. It comprises databases of several thousand species and has information on genes and proteins, small molecule ligands, pathways and hierarchical relationships. These are present in classified order in KEGG GENES, KEGG LIGAND, KEGG PATHWAY and KEGG BRITE. The KEGG also serves as a knowledge base that connects genomes to systems functioning. KEGG provides information at the systems, genomic and chemical levels. 1.1 SYSTEMS INFORMATION KEGG PATHWAY: Metabolic and reaction networks, cellular processes KEGG BRITE: Functional hierarchies KEGG MODULES: Pathway modules. KEGG DISEASES: Diseases. 1.2 GENOMIC INFORMATION GENES -- KEGG ORTHOLOGY (KO): Ortholog groups based on KEGG PATHWAY and KEGG BRITE. GENES: Gene catalogs of complete genomes with manual annotation. DGENES: Gene catalogs of draft genomes with automatic annotation. EGENES: Gene catalogs of EST with automatic annotation. GENOME: Genome maps and organism information. SSDB: Sequence similarities with best hit information for identifying Ortholog/Paralog clusters and conserved gene clusters. Joint Initiative of IITs and IISc Funded by MHRD Page 3 of 14

4 1.3 CHEMICAL INFORMATION LIGAND COMPOUND: Chemical compounds. DRUG: Drugs approved in the U.S. and in Japan. GLYCAN: Glycans. REACTION: Chemical reactions. RPAIR: Chemical structure transformation patterns. ENZYME: Enzyme nomenclature. 2 KEGG PATHWAY The KEGG Pathway Database accommodates a large collection of reference diagrams, or maps, each corresponding to a known biological network of functional significance. Though each map is represented for multiple species, one can also view species specific by choosing specific genes and colouring them. Let us now take an exercise Open the KEGG Genome Net Web page at 1. Go to the Database column of the table on the top left. Joint Initiative of IITs and IISc Funded by MHRD Page 4 of 14

5 2. Click on the KEGG PATHWAY 3. You can now see a list of KEGG s pathways organized in a hierarchical manner. Each level of the hierarchy shown here corresponds to an increasingly specific view of the biological network. Joint Initiative of IITs and IISc Funded by MHRD Page 5 of 14

6 4. We can either give a text search or can click onto the hierarchy given. 5. Select glycolysis/gluconeogenesis from metabolism and this takes to the pathway map. 6. Each enzyme in this page is given with its E.C number. 7. By clicking any one of the E.C. number it takes to the page which displays the information of the whole enzyme with its reaction, products formed, pathway involved, its orthology and the gene information. Joint Initiative of IITs and IISc Funded by MHRD Page 6 of 14

7 3 KEGG LIGAND KEGG LIGAND comprises four databases: COMPOUND, GLYCAN, REACTION, and ENZYME. COMPOUND is a database of chemical structures of most known metabolic compounds and some pharmaceutical and environmental compounds; GLYCAN is a database of carbohydrate structures; REACTION is a database of reaction formulas for enzymic reactions; and ENZYME is a database of enzyme nomenclatures. 1. Open the KEGG database using the URL Click the LIGAND link to bring up the KEGG LIGAND Database search page. 2. The search is made by text search by entering the molecule directly in KEGG COMPOUND search. Joint Initiative of IITs and IISc Funded by MHRD Page 7 of 14

8 3. Example search for benzene and it takes to the number of entries in which one of the ID from KEGG COMPOUND is selected. 4. Clicking on any one of the structure gives the information such as the Entry ID, additional names of the compound, formula, structure (here the structure can be downloaded as the mol file), reaction, pathway involved, enzymes and the link to the other databases. Joint Initiative of IITs and IISc Funded by MHRD Page 8 of 14

9 4 KEGG BRITE/KEGG GENES/KEGG ENZYME KEGG BRITE gives the functional hierarchies representing our knowledge on various aspects of biological systems. 1. Open the KEGG database using the URL 2. Click on KEGG ligand and select the compound (Ex: benzene). 3. Then click on the Enzyme under the Ligand database. Joint Initiative of IITs and IISc Funded by MHRD Page 9 of 14

10 4. Click on KEGG BRITE from the ligand database and search for functional hierarchies and ontologies for your query protein or enzyme. Joint Initiative of IITs and IISc Funded by MHRD Page 10 of 14

11 5. Click on KEGG GENES to get the gene information of an organism or a gene such as its sequence, Entry ID, gene ID, definition of the gene, chromosomal position and even the hierarchy. Find the pathway of p53 gene using KEGG: Joint Initiative of IITs and IISc Funded by MHRD Page 11 of 14

12 It is done by the text search given in the web page. This gives the information about the pathway. By clicking the link map05218 under pathway map it takes to the page of pathway map where the reactions and the enzymes involved can be visualised. Joint Initiative of IITs and IISc Funded by MHRD Page 12 of 14

13 As done above the pathway of the gene BCL2 can also be viewed in KEGG pathway for the map ID map Joint Initiative of IITs and IISc Funded by MHRD Page 13 of 14

14 These sets of exercises give us an overview of pathway mapping.let us explore more using CytoScape and Cell Designer in the next few classes. Joint Initiative of IITs and IISc Funded by MHRD Page 14 of 14

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