Monday, August 20, 2012

Pathway



http://www.genome.jp/kegg/pathway.html#global


Pathway Maps

KEGG PATHWAY is a collection of manually drawn pathway maps (see new mapschange history, and last updates) representing our knowledge on the molecular interaction and reaction networks for:
0. Global Map
1. Metabolism
    Carbohydrate   Energy   Lipid   Nucleotide   Amino acid   Other amino acid   Glycan
    Cofactor/vitamin   Terpenoid/PK   Other secondary metabolite   Xenobiotics   Overview
2. Genetic Information Processing
3. Environmental Information Processing
4. Cellular Processes
5. Organismal Systems
6. Human Diseases
and also on the structure relationships (KEGG drug structure maps) in:
7. Drug Development

Pathway Mapping

KEGG PATHWAY mapping is the process to map molecular datasets, especially large-scale datasets in genomics, transcriptomics, proteomics, and metabolomics, to the KEGG pathway maps for biological interpretaion of higher-level systemic functions.


0. Global Map

0.1 Metabolism
Metabolic pathways [zoom out]
Biosynthesis of secondary metabolites [zoom out]
Launch KEGG Atlas
Launch KEGG Atlas


1. Metabolism

1.1 Carbohydrate Metabolism
Glycolysis / Gluconeogenesis
Citrate cycle (TCA cycle)
Pentose phosphate pathway
Pentose and glucuronate interconversions
Fructose and mannose metabolism
Galactose metabolism
Ascorbate and aldarate metabolism
Starch and sucrose metabolism
Amino sugar and nucleotide sugar metabolism
Pyruvate metabolism
Glyoxylate and dicarboxylate metabolism
Propanoate metabolism
Butanoate metabolism
C5-Branched dibasic acid metabolism
Inositol phosphate metabolism
Enzymes
Compounds with biological roles
1.2 Energy Metabolism
Oxidative phosphorylation
Photosynthesis
Photosynthesis - antenna proteins
Carbon fixation in photosynthetic organisms
Reductive carboxylate cycle in photosynthetic bacteria
Methane metabolism Major update!
Nitrogen metabolism
Sulfur metabolism

Photosynthesis proteins
1.3 Lipid Metabolism
Fatty acid biosynthesis
Fatty acid elongation in mitochondria
Fatty acid metabolism
Synthesis and degradation of ketone bodies
Steroid biosynthesis
Primary bile acid biosynthesis
Secondary bile acid biosynthesis
Steroid hormone biosynthesis
Glycerolipid metabolism
Glycerophospholipid metabolism
Ether lipid metabolism
Sphingolipid metabolism
Arachidonic acid metabolism
Linoleic acid metabolism
alpha-Linolenic acid metabolism
Biosynthesis of unsaturated fatty acids
Lipids
Lipid biosynthesis proteins
1.4 Nucleotide Metabolism
Purine metabolism
Pyrimidine metabolism
1.5 Amino Acid Metabolism
Alanine, aspartate and glutamate metabolism
Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
Valine, leucine and isoleucine degradation
Valine, leucine and isoleucine biosynthesis
Lysine biosynthesis
Lysine degradation
Arginine and proline metabolism
Histidine metabolism
Tyrosine metabolism
Phenylalanine metabolism
Tryptophan metabolism
Phenylalanine, tyrosine and tryptophan biosynthesis
1.6 Metabolism of Other Amino Acids
beta-Alanine metabolism
Taurine and hypotaurine metabolism
Phosphonate and phosphinate metabolism
Selenoamino acid metabolism
Cyanoamino acid metabolism
D-Glutamine and D-glutamate metabolism
D-Arginine and D-ornithine metabolism
D-Alanine metabolism
Glutathione metabolism
1.7 Glycan Biosynthesis and Metabolism
N-Glycan biosynthesis
High-mannose type N-glycan biosynthesis
O-Glycan biosynthesis
O-Mannosyl glycan biosynthesis
Glycosaminoglycan biosynthesis - chondroitin sulfate
Glycosaminoglycan biosynthesis - heparan sulfate
Glycosaminoglycan biosynthesis - keratan sulfate
Glycosaminoglycan degradation
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
Glycosphingolipid biosynthesis - lacto and neolacto series
Glycosphingolipid biosynthesis - globo series
Glycosphingolipid biosynthesis - ganglio series
Lipopolysaccharide biosynthesis
Peptidoglycan biosynthesis
Other glycan degradation
KEGG GLYCAN

Composite structure map
Monosaccharide codes

Glycosyltransferases
Proteoglycans
LPS biosynthesis proteins
1.8 Metabolism of Cofactors and Vitamins
Thiamine metabolism
Riboflavin metabolism
Vitamin B6 metabolism
Nicotinate and nicotinamide metabolism
Pantothenate and CoA biosynthesis
Biotin metabolism
Lipoic acid metabolism
Folate biosynthesis
One carbon pool by folate
Retinol metabolism
Porphyrin and chlorophyll metabolism
Ubiquinone and other terpenoid-quinone biosynthesis
1.9 Metabolism of Terpenoids and Polyketides
Terpenoid backbone biosynthesis
Monoterpenoid biosynthesis
Sesquiterpenoid biosynthesis
Diterpenoid biosynthesis
Carotenoid biosynthesis
Brassinosteroid biosynthesis
Insect hormone biosynthesis
Zeatin biosynthesis
Limonene and pinene degradation
Geraniol degradation
Type I polyketide structures
Biosynthesis of 12-, 14- and 16-membered macrolides
Biosynthesis of ansamycins
Biosynthesis of type II polyketide backbone
Biosynthesis of type II polyketide products
Tetracycline biosynthesis
Polyketide sugar unit biosynthesis
Nonribosomal peptide structures
Biosynthesis of siderophore group nonribosomal peptides
Biosynthesis of vancomycin group antibiotics
1.10 Biosynthesis of Other Secondary Metabolites
Phenylpropanoid biosynthesis
Stilbenoid, diarylheptanoid and gingerol biosynthesis
Flavonoid biosynthesis
Flavone and flavonol biosynthesis
Anthocyanin biosynthesis
Isoflavonoid biosynthesis
Indole alkaloid biosynthesis
Isoquinoline alkaloid biosynthesis
Tropane, piperidine and pyridine alkaloid biosynthesis
Acridone alkaloid biosynthesis
Caffeine metabolism
Betalain biosynthesis
Glucosinolate biosynthesis
Benzoxazinoid biosynthesis
Penicillin and cephalosporin biosynthesis
beta-Lactam resistance
Streptomycin biosynthesis
Butirosin and neomycin biosynthesis
Clavulanic acid biosynthesis
Puromycin biosynthesis
Novobiocin biosynthesis
Phytochemical compounds
1.11 Xenobiotics Biodegradation and Metabolism
Caprolactam degradation
Biphenyl degradation
Toluene and xylene degradation
gamma-Hexachlorocyclohexane degradation
3-Chloroacrylic acid degradation
1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
2,4-Dichlorobenzoate degradation
1,2-Dichloroethane degradation
Tetrachloroethene degradation
Styrene degradation
1,4-Dichlorobenzene degradation
Naphthalene and anthracene degradation
Ethylbenzene degradation
Fluorene degradation
Carbazole degradation
Benzoate degradation via CoA ligation
Benzoate degradation via hydroxylation
Atrazine degradation
Bisphenol A degradation
1- and 2-Methylnaphthalene degradation
Trinitrotoluene degradation
Fluorobenzoate degradation
Metabolism of xenobiotics by cytochrome P450
Drug metabolism - cytochrome P450
Drug metabolism - other enzymes
1.12 Overview
Overview of biosynthetic pathways
Biosynthesis of plant secondary metabolites
Biosynthesis of phenylpropanoids
Biosynthesis of terpenoids and steroids
Biosynthesis of alkaloids derived from shikimate pathway
Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
Biosynthesis of alkaloids derived from histidine and purine
Biosynthesis of alkaloids derived from terpenoid and polyketide
Biosynthesis of plant hormones


2. Genetic Information Processing

2.1 Transcription
RNA polymerase
Basal transcription factors
Spliceosome

Transcription factors
Spliceosome
2.2 Translation
Ribosome
Aminoacyl-tRNA biosynthesis
Ribosome
Translation factors
2.3 Folding, Sorting and Degradation
Protein export
Protein processing in endoplasmic reticulum New!
SNARE interactions in vesicular transport
Ubiquitin mediated proteolysis
Sulfur relay system New!
Proteasome
RNA degradation
Chaperones and folding catalysts
SNAREs
Ubiquitin system
Proteasome
2.4 Replication and Repair
DNA replication
Base excision repair
Nucleotide excision repair
Mismatch repair
Homologous recombination
Non-homologous end-joining
DNA replication proteins
Chromosome
DNA repair and recombination proteins


3. Environmental Information Processing

3.1 Membrane Transport
ABC transporters
Phosphotransferase system (PTS)
Bacterial secretion system
Transporters
Secretion system
Bacterial toxins
3.2 Signal Transduction
Two-component system
MAPK signaling pathway
MAPK signaling pathway - fly
MAPK signaling pathway - yeast
ErbB signaling pathway
Wnt signaling pathway
Notch signaling pathway
Hedgehog signaling pathway
TGF-beta signaling pathway
VEGF signaling pathway
Jak-STAT signaling pathway
Calcium signaling pathway
Phosphatidylinositol signaling system
mTOR signaling pathway
Two-component system
3.3 Signaling Molecules and Interaction
Neuroactive ligand-receptor interaction
Cytokine-cytokine receptor interaction
ECM-receptor interaction
Cell adhesion molecules (CAMs)
G protein-coupled receptors
Enzyme-linked receptors
Cytokine receptors / Cytokines
Nuclear receptors
Ion channels
GTP-binding proteins
CAMs / CAM ligands
Cellular antigens
Glycan binding proteins


4. Cellular Processes

4.1 Transport and Catabolism
Endocytosis
Phagosome
Lysosome
Peroxisome
Regulation of autophagy
4.2 Cell Motility
Bacterial chemotaxis
Flagellar assembly
Regulation of actin cytoskeleton
Bacterial motility proteins

Cytoskeleton proteins
4.3 Cell Growth and Death
Cell cycle
Cell cycle - yeast
Cell cycle - Caulobacter
Meiosis - yeast
Oocyte meiosis
Apoptosis
p53 signaling pathway
4.4 Cell Communication
Focal adhesion
Adherens junction
Tight junction
Gap junction


5. Organismal Systems

5.1 Immune System
Hematopoietic cell lineage
Complement and coagulation cascades
Toll-like receptor signaling pathway
NOD-like receptor signaling pathway
RIG-I-like receptor signaling pathway
Cytosolic DNA-sensing pathway
Natural killer cell mediated cytotoxicity
Antigen processing and presentation
T cell receptor signaling pathway
B cell receptor signaling pathway
Fc epsilon RI signaling pathway
Fc gamma R-mediated phagocytosis
Leukocyte transendothelial migration
Intestinal immune network for IgA production
Chemokine signaling pathway
5.2 Endocrine System
Insulin signaling pathway
Adipocytokine signaling pathway
PPAR signaling pathway
GnRH signaling pathway
Progesterone-mediated oocyte maturation
Melanogenesis
Renin-angiotensin system
5.3 Circulatory System
Cardiac muscle contraction
Vascular smooth muscle contraction
5.4 Digestive System
Salivary secretion
Gastric acid secretion
Pancreatic secretion New!
Carbohydrate digestion and absorption New!
Protein digestion and absorption New!
5.5 Excretory System
Aldosterone-regulated sodium reabsorption
Vasopressin-regulated water reabsorption
Proximal tubule bicarbonate reclamation
Collecting duct acid secretion
5.6 Nervous System
Long-term potentiation
Long-term depression
Neurotrophin signaling pathway
5.7 Sensory System
Phototransduction
Phototransduction - fly
Olfactory transduction
Taste transduction
5.8 Development
Dorso-ventral axis formation
Axon guidance
5.9 Environmental Adaptation
Circadian rhythm - mammal
Circadian rhythm - fly
Circadian rhythm - plant
Plant-pathogen interaction


6. Human Diseases

6.1 Cancers
Pathways in cancer (overview)
Colorectal cancer
Pancreatic cancer
Glioma
Thyroid cancer
Acute myeloid leukemia
Chronic myeloid leukemia
Basal cell carcinoma
Melanoma
Renal cell carcinoma
Bladder cancer
Prostate cancer
Endometrial cancer
Small cell lung cancer
Non-small cell lung cancer
KEGG DISEASE

Human diseases
ICD-10 disease classification
6.2 Immune System Diseases
Asthma
Systemic lupus erythematosus
Autoimmune thyroid disease
Allograft rejection
Graft-versus-host disease
Primary immunodeficiency
6.3 Neurodegenerative Diseases
Alzheimer's disease
Parkinson's disease
Amyotrophic lateral sclerosis (ALS)
Huntington's disease
Prion diseases
6.4 Cardiovascular Diseases
Hypertrophic cardiomyopathy (HCM)
Arrhythmogenic right ventricular cardiomyopathy (ARVC)
Dilated cardiomyopathy (DCM)
Viral myocarditis
6.5 Metabolic Diseases
Type I diabetes mellitus
Type II diabetes mellitus
Maturity onset diabetes of the young
6.6 Infectious Diseases
Vibrio cholerae infection
Vibrio cholerae pathogenic cycle
Epithelial cell signaling in Helicobacter pylori infection
Pathogenic Escherichia coli infection
Shigellosis
Staphylococcus aureus infection New!
Bacterial invasion of epithelial cells
Hepatitis C New!
Amoebiasis
Malaria
Toxoplasmosis New!
Leishmaniasis
Chagas disease


7. Drug Development

7.1 Chronology: Antibiotics
Penicillins
Cephalosporins - parenteral agents
Cephalosporins - oral agents
Aminoglycosides
Tetracyclines
Macrolides and ketolides
Quinolones
Rifamycins
KEGG DRUG

ATC classification (WHO)
Therapeutic category of drugs (Japan)
USP drug classification (USA)
7.2 Chronology: Antineoplastics
Antineoplastics - alkylating agents
Antineoplastics - antimetabolic agents
Antineoplastics - agents from natural products
Antineoplastics - hormones
Antineoplastics - protein kinases inhibitors
7.3 Chronology: Nervous System Agents
Hypnotics
Anxiolytics
Anticonvulsants
Local analgesics
Opioid analgesics
Antipsychotics
Antipsychotics - phenothiazines
Antipsychotics - butyrophenones
Antidepressants
7.4 Chronology: Other Drugs
Sulfonamide derivatives - sulfa drugs
Sulfonamide derivatives - diuretics
Sulfonamide derivatives - hypoglycemic agents
Antiarrhythmic drugs
Antacids
Antivirals
Immunosuppressive agents
Osteoporosis drugs
Antimigraines
7.5 Target Based Classification: G Protein-Coupled Receptors
Cholinergic and anticolinergic drugs
alpha-Adrenergic receptor agonists/antagonists
beta-Adrenergic receptor agonists/antagonists
Dopamine receptor agonists/antagonists
Histamine H1 receptor antagonists
Histamine H2/H3 receptor agonists/antagonists
Serotonin receptor agonists/antagonists
Eicosanoid receptor agonists/antagonists New!
Opioid receptor agonists/antagonists
Angiotensin receptor and endothelin receptor antagonists New!
G protein-coupled receptors
7.6 Target Based Classification: Nuclear Receptors
Glucocorticoid and mineralocorticoid receptor agonists/antagonists
Progesterone, androgen and estrogen receptor agonists/antagonists
Retinoic acid receptor (RAR) and retinoid X receptor (RXR) agonists/antagonists
Peroxisome proliferator-activated receptor (PPAR) agonists
Nuclear receptors
7.7 Target Based Classification: Ion Channels
Nicotinic cholinergic receptor antagonists
Calcium channel blocking agents
Ion channels
7.8 Target Based Classification: Enzymes
Catecholamine transferase inhibitors
Cyclooxygenase inhibitors
HIV protease inhibitors
Renin-angiotensin system inhibitors Major update!
7.9 Structure Based Classification
Azoles
Quinolines
Statins
Eicosanoids
Prostaglandins
7.10 Skeleton Based Classification
Benzoic acid family
2-Aminothiazole family
1,2-Diphenyl substitution family
Furan family
Naphthalene family
Sulfonamide family
Butyrophenone family
Benzodiazepine family


Best Wishes: Dr.Ehab Aboueladab, Tel:01007834123 Email:ehab10f@gmail.com,ehababoueladab@yahoo.com ehab fathy aboueladab
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