KEGG Introduction 2021 PDF

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Introduction on how to use KEGG for the practical modules...

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KEGG intro (Metabolism) Spring 2021

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Ming Wu

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database resource that integrates genomic, chemical (metabolic pathways) and systemic functional information. Access (free): https://www.genome.jp/kegg Go to Google, type in KEGG, you are there. It is a database of the biological system, consisting of the genomic and chemical information with a complete set of building blocks (genes and molecules); the network information including molecular wiring diagrams (interaction/reaction networks, so called metabolic pathways); hierarchical classifications (relation networks) to represent high-level functions; also disease and drug information (health information) as perturbations to the biological system.

The KEGG Database KEGG is an integrated database resource consisting of sixteen databases shown below. They are broadly categorized into systems information, genomic information, chemical information and health information, which are distinguished by color coding of web pages. Category

Database

Content

KEGG PATHWAY Systems KEGG BRITE information KEGG MODULE

KEGG pathway maps

KEGG ORTHOLOGY (KO) Genomic information KEGG GENES KEGG GENOME

Functional orthologs

KEGG COMPOUND

Color

BRITE hierarchies and tables KEGG modules and reaction modules

Genes and proteins KEGG organisms and viruses Small molecules

Glycans Chemical KEGG GLYCAN information KEGG REACTION / RCLASS Reactions and reaction class KEGG ENZYME

Enzyme nomenclature

KEGG NETWORK

Disease-related network variations

KEGG VARIANT Health information KEGG DISEASE

Human gene variants Human diseases

KEGG DRUG / DGROUP Drugs and drug groups Chemical information category is collectively called KEGG LIGAND Health information category integrated with drug labels is called KEGG MEDICUS

KEGG intro (Metabolism) Spring 2021

Ming Wu

In this unit, you need to be able to use KEGG database to complete your lab report in the workshops. The following is a brief guide for you (each student should spend time on KEGG, familiarise with the webpage). •

By clicking KEGG PATHWAY, you will go to KEGG pathway page, you can then search a particular pathway you like. For example, enter Keyword: glycolysis, click Organism, then type Homo sapiens, select Homo sapiens has, then click Go.

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You will be given a set of clinical symptoms, then you should analyse them according to what you will have learned from the lectures, finally arrive at a likely diagnosis. In this task, you need to focus on metabolic diseases (because you are learning Metabolism, you should not have a diagnosis in an infectious disease). Look at an example below: Symptoms: Intense joint pain, particularly in the big toe, inflammation and redness in the affected joint. Diagnosis: The patient likely suffers gout. Search the web (google search should be helpful) and get some information of gout. It is related to purine metabolism. Uric acid (urate) is a metabolite of purine metabolism, its accumulation in joints would lead to gout. You can go to KEGG pathway, search purine metabolism to get the pathway network. You can also search KEGG compound for uric acid to get the metabolic pathway for purine metabolism. You can also search KEGG disease for gout, to learn more about the health problem, the drugs for its treatment, etc. Most importantly, you need to fully understand the lecture contents in order to have yourself in the right direction for arriving at a correct diagnosis.

KEGG intro (Metabolism) Spring 2021

Ming Wu

Appendix info The following figure gives you some very basics on KEGG pathway:

Figure 1. Portion of the KEGG “Glycolysis/Gluconeogenesis” pathway map. The round areas filled with text are hyperlinks to other KEGG pathway maps. The rectangles represent individual enzymes (EC numbers shown in a box), and small circles represent individual metabolites. When displayed in a web browser, these are mouse-sensitive hyperlinks that lead to web pages describing the specific enzyme/metabolite.

KEGG intro (Metabolism) Spring 2021

Ming Wu

All maps are drawn with the notation shown below:...