PathWhiz

PathWhiz ID	Pathway	Meta Data
PW123892 View Pathway	drug action EXAMPLE: Irinotecan Metabolism 1589933802 Homo sapiens BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: May 19, 2020 at 18:16 Last Updated: May 19, 2020 at 18:16
PW000733 View Pathway	metabolic EXAMPLE: Ketone Body Metabolism Homo sapiens Acetoacetate, beta-hydroxybutyrate, and acetone collectively are called ketone bodies. The first two are synthesized from acetyl-CoA, in the mitochondria of liver cells; acetone is formed by spontaneous decarboxylation of acetoacetate. Ketone body synthesis (Ketogenesis) in liver is effectively irreversible because the enzyme that catalyzes the conversion of acetoacetate to acetoacetyl-CoA is not present in liver cells. Ketone bodies, unlike fatty acids and triglycerides, are water-soluble. They are exported from the liver, and are taken up by other tissues, notably brain and skeletal and cardiac muscle. Extrahepatic tissues utilize ketone bodies by converting the beta-hydroxybutyrate successively to acetoacetate, acetoacetatyl-CoA, finally to acetyl-CoA which is oxidized via the TCA cycle to yield energy. In a normal person, this pathway of ketone body synthesis and utilization is most active during extended periods of fasting. Under these conditions, mobilization and breakdown of stored fatty acids generates abundant acetyl-CoA acetyl-CoA in liver cells for synthesis of ketone bodies, and their utilization in other tissues minimizes the demand of these tissues for glucose. The levels of acetone in ketone bodies are much lower than those of acetoacetic acid and beta-hydroxybutyric acid. Acetone cannot be converted back to acetyl-CoA, and is excreted in urine, or breathed out through the lungs. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: December 29, 2014 at 17:32 Last Updated: December 29, 2014 at 17:32
PW000742 View Pathway	physiological EXAMPLE: Kidney Function Homo sapiens Kidneys are regulatory organs involved in removing wastes from the blood, hormone production, nutrient reabsorption, and regulating electrolyte concentrations, acid-base balance, extracellular fluid volume, and blood pressure. The early proximal tubule is where glucose, amino acids, sodium, chlorine, phosphate, bicarbonate, and water are reabsorbed. Only water is reabsorbed in the thin descending loop of Henle, while sodium, chlorine and potassium are reabsorbed in the thick ascending loop of Henle. Sodium and chlorine are also reabsorbed in the early distal convoluted tubule. Finally, sodium and water are reabsorbed in the collecting tubules. Blood pressure is regulated by the hormones angiotensin II and aldosterone, which increases sodium chloride reabsorption. This results in an expansion of the extracellular fluid compartment, thus increasing blood pressure. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: December 29, 2014 at 20:53 Last Updated: December 29, 2014 at 20:53
PW000743 View Pathway	physiological EXAMPLE: Muscle/Heart Contraction Homo sapiens Muscle contractions occur when the myocyte is depolarized enough for an action potential to occur. Depolarization is caused by acetylcholine released from the adjacent motor neuron, which activates nicotinic acetylcholine receptors and opens the sodium/potassium channel. The fast influx of sodium and slow efflux of potassion trigger the action potential. This action potential activates L-type voltage-dependent calcium channels on the membrane and ryanodine receptors on the sarcoplasmic reticulum, both which cause calcium ions to be released into the cytosol. In smooth muscle, ionic calcium induces muscle contraction by binding to and activating myosin light chain kinase, while in striated muscle contraction results from ionic calcium binding to and activating troponin C. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: December 29, 2014 at 20:54 Last Updated: December 29, 2014 at 20:54
PW000744 View Pathway	physiological EXAMPLE: Pancreas Function Homo sapiens The pancreas is a glandular organ in the digestive system and endocrine system of vertebrates. It is both an endocrine gland producing several important hormones, including insulin, glucagon, somatostatin, and pancreatic polypeptide, and a digestive organ, secreting pancreatic juice containing digestive enzymes that assist the absorption of nutrients and the digestion in the small intestine. These enzymes help to further break down the carbohydrates, proteins, and lipids in the chyme. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: December 29, 2014 at 20:55 Last Updated: December 29, 2014 at 20:55
PW000747 View Pathway	signaling EXAMPLE: Vasopressin Regulation of Water Homeostasis Homo sapiens The V2 receptor is expressed in the kidney tubule, predominantly in the distal convoluted tubule and collecting ducts, where its primary property is to respond to the pituitary hormone arginine vasopressin (AVP) by stimulating mechanisms that concentrate the urine and maintain water homeostasis in the organism. When the function of this gene is lost, the disease Nephrogenic Diabetes Insipidus (NDI) results. The V2 receptor is also expressed outside the kidney although its tissue localization is uncertain. When these ‘extrarenal receptors’ are stimulated by infusion of a V2 selective agonist (dDAVP), a variety of clotting factors are released into the bloodstream. The physiologic importance of this property is not known. The V2 receptor activates G(s) proteins which lead to the activation of adenylyl cyclase which produces the secondary messenger cAMP. cAMP activates PKA (protein kinase A) which phosphorylates downstream effectors that lead to a specific cellular response. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: December 29, 2014 at 21:00 Last Updated: December 29, 2014 at 21:00
PW000735 View Pathway	metabolic EXAMPLE: Vitamin K Metabolism Homo sapiens Vitamin K describes a group of lipophilic, hydrophobic vitamins that exist naturally in two forms (and synthetically in three others): vitamin K1, which is found in plants, and vitamin K2, which is synthesized by bacteria. Vitamin K is an important dietary component because it is necessary as a cofacter in the activation of vitamin K dependent proteins. Metabolism of vitamin K occurs mainly in the liver. In the first step, vitamin K is reduced to its quinone form by a quinone reductase such as NAD(P)H dehydrogenase. Reduced vitamin K is the form required to convert vitamin K dependent protein precursors to their active states. It acts as a cofactor to the integral membrane enzyme vitamin K-dependent gamma-carboxylase (along with water and carbon dioxide as co-substrates), which carboxylates glutamyl residues to gamma-carboxy-glutamic acid residues on certain proteins, activating them. Each converted glutamyl residue produces a molecule of vitamin K epoxide, and certain proteins may have more than one residue requiring carboxylation. To complete the cycle, the vitamin K epoxide is returned to vitamin K via the vitamin K epoxide reductase enzyme, also an integral membrane protein. The vitamin K dependent proteins include a number of important coagulation factors, such as prothrombin. Thus, warfarin and other coumarin drugs act as anticoagulants by blocking vitamin K epoxide reductase. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: December 29, 2014 at 20:38 Last Updated: December 29, 2014 at 20:38
PW012936 View Pathway	metabolic Examplecc Homo sapiens BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Guest: Anonymous Created On: March 13, 2017 at 04:10 Last Updated: March 13, 2017 at 04:10
PW000441 View Pathway	protein Excitatory Neural Signalling Through 5-HTR 4 and Serotonin Homo sapiens The 5-HT4 receptor is primarily found in the CNS, GI tract, and PNS. Peripheral receptors have important roles in the function of many organ responses (alimentary tract, urinary bladder, heart, and adrenal gland). Alimentary tract receptors have a role in smooth muscle tone, mucosal electrolyte secretion, and the peristaltic reflex. Urinary bladder receptors control cholinergic/purinergic transmission. Atrial heart receptors produce positive inotropy and tachycardia that can precipitate arrhythmias. This receptor is also thought to have roles in anxiety, appetite, GI motility, learning, memory, mood, and respiration. The 5-HT4 receptor activates G(s) proteins which lead to the activation of adenylyl cyclase which produces the secondary messenger cAMP. cAMP activates PKA (protein kinase A) which phosphorylates downstream effectors that lead to a specific cellular response. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: WishartLab Created On: August 22, 2013 at 10:46 Last Updated: August 22, 2013 at 10:46
PW109211 View Pathway	protein Excitatory Neural Signalling Through 5-HTR 4 and Serotonin Bos taurus The 5-HT4 receptor is primarily found in the CNS, GI tract, and PNS. Peripheral receptors have important roles in the function of many organ responses (alimentary tract, urinary bladder, heart, and adrenal gland). Alimentary tract receptors have a role in smooth muscle tone, mucosal electrolyte secretion, and the peristaltic reflex. Urinary bladder receptors control cholinergic/purinergic transmission. Atrial heart receptors produce positive inotropy and tachycardia that can precipitate arrhythmias. This receptor is also thought to have roles in anxiety, appetite, GI motility, learning, memory, mood, and respiration. The 5-HT4 receptor activates G(s) proteins which lead to the activation of adenylyl cyclase which produces the secondary messenger cAMP. cAMP activates PKA (protein kinase A) which phosphorylates downstream effectors that lead to a specific cellular response. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: Ana Marcu Created On: August 31, 2018 at 12:33 Last Updated: August 31, 2018 at 12:33