A quodlibet is a piece of music combining several different melodies, usually popular tunes, in counterpoint and often a light-hearted, humorous manner. The term is Latin, meaning "whatever" or literally, "what pleases."
QUODLIBET is a computer program that creates, edits and queries biomedical networks. In addition to providing information about genetic-protein-phenotype interactions QUODLIBET also allows for additional information to be harvested, including data on the effects of natural products on gene-protein expression.
Unlike most biochemical pathway/network depiction programs QUODLIBET actually thinks. It analyzes the network and reports on many graph functions including betweeness centralities, page-ranks, and cluster coefficients. This allows an immediate understand of which nodes are acting in a critically important role in the network. Many of these same alogrithms are used by social networking platforms like FaceBook and search engines such as Google.
A section of a Quodlibet Map showing genes with highly connected nodes (yellow circles) and associated agens (green hexagons) .
QUODLIBET was conceived, designed and programmed by Peter D'Adamo.
It was designed to be simple, easy to use and fun to edit and develop in. Because it is web-based, no special software is required, other than a modern browser and a decent Internet connection. QUODLIBET runs under the DataPunk platform and is open-access. Curators can use the extensive editing tools to add to, alter, or create entirely new networks.
Since the project is community-based, we are always looking for volunteers who are interested in helping out. Volunteers need not have any medical or super computer skills, just a passion for exactitude and a desire learn more about the genetics and biology.
To learn more about QUODLIBET, you can download the User Guide, the Editor Guide and visit the Community Forums. The Sandbox is a great place to practice developing and editing maps. You can log in with the username guest and the password quodlibet to gain access to the editor.
|Quodlibet Network as of : Fri Oct 24 11:21:26 2014 |
- 4409 nodes connected by 5467 edges in 60 metabolic maps
Current Metabolic Maps
- Adipocytokine signaling pathway - Homo sapiens (human)
Increased adipocyte volume and number are positively correlated with leptin production, and negatively correlated with production of adiponectin. Leptin is an important regulator of energy intake and metabolic rate primarily by acting at hypothalamic nuclei.
- Alzheimer's disease - Homo sapiens (human)
Alzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs).
- Amino sugar and nucleotide sugar metabolism
Glycosaminoglycans (GAGs) or mucopolysaccharides are long unbranched polysaccharides consisting of a repeating disaccharide unit. Members of the glycosaminoglycan family vary in the type of hexosamine, hexose or hexuronic acid unit they contain (e.
- Apoptosis - Homo sapiens (human)
Apoptosis is a genetically controlled mechanisms of cell death involved in the regulation of tissue homeostasis. The 2 major pathways of apoptosis are the extrinsic (Fas and other TNFR superfamily members and ligands) and the intrinsic (mitochondria-associated) pathways, both of which are found in the cytoplasm.
- Acute myeloid leukemia - Homo sapiens (human)
Acute myeloid leukemia (AML) is a disease that is characterized by uncontrolled proliferation of clonal neoplastic cells and accumulation in the bone marrow of blasts with an impaired differentiation program. AML accounts for approximately 80% of all adult leukemias and remains the most common cause of leukemia death.
- Ascorbate and aldarate metabolism - Homo sapiens (human)
Ascorbate (an ion of ascorbic acid) is required for a range of essential metabolic reactions in all animals and plants. Vitamin C or L-ascorbic acid or L-ascorbate is an essential nutrient for humans and certain other animal species.
- Autophagy - Homo sapiens (human)
Autophagy is a process of self-digestion that occurs in eukaryotic cells. Autophagy involves the formation of a membrane around a region of the cytoplasm, sequestering macromolecules like proteins and organelles, and the fusion of the resultant vesicle with a lysosome in which the contents are degraded.
- B cell receptor signaling pathway - Homo sapiens (human)
B cells are an important component of adaptive immunity. They produce and secrete millions of different antibody molecules, each of which recognizes a different (foreign) antigen.
- Bisphenol A (BPA): Metabolic effects and degradation
The bisphenols are a group of chemical compounds with two hydroxyphenyl functionalities. Most of them based on diphenylmethane.
- Chemokine signaling pathway - Homo sapiens (human)
Inflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for the cell trafficking and thus are vital for protective host response.
- Pathways in Cancer
Cancer arises from the stepwise accumulation of genetic changes that confer upon an incipient neoplastic cell the properties of unlimited, self-sufficient growth and resistance to normal homeostatic regulatory mechanisms. Advances in human genetics and molecular and cellular biology have identified a collection of cell phenotypes that are required for malignant transformation.
- Colorectal cancer - Homo sapiens (human)
Colorectal cancer (CRC) is the second largest cause of cancer-related deaths in Western countries. CRC arises from the colorectal epithelium as a result of the accumulation of genetic alterations in defined oncogenes and tumour suppressor genes (TSG).
- Cysteine and methionine metabolism - Homo sapiens (human)
Cysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups.
- Citrate cycle (TCA cycle) - Homo sapiens (human)
The citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form of acetate, derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids.
- Complement and coagulation cascades - Homo sapiens (human)
The complement system is a proteolytic cascade in blood plasma and a mediator of innate immunity, a nonspecific defense mechanism against pathogens. There are three pathways of complement activation: the classical pathway, the lectin pathway, and the alternative pathway.
- ErbB signaling pathway - Homo sapiens (human)
The ErbB family of receptor tyrosine kinases (RTKs) couples binding of extracellular growth factor ligands to intracellular signaling pathways regulating diverse biologic responses, including proliferation, differentiation, cell motility, and survival. Ligand binding to the four closely related members of this RTK family -epidermal growth factor receptor (EGFR, also known as ErbB-1 or HER1), ErbB-2 (HER2), ErbB-3 (HER3), and ErbB-4 (HER4)-induces the formation of receptor homo- and heterodimers and the activation of the intrinsic kinase domain, resulting in phosphorylation on specific tyrosine residues (pY) within the cytoplasmic tail.
- Fc epsilon RI signaling pathway - Homo sapiens (human)
Fc epsilon RI-mediated signaling pathways in mast cells are initiated by the interaction of antigen (Ag) with IgE bound to the extracellular domain of the alpha chain of Fc epsilon RI. The activation pathways are regulated both positively and negatively by the interactions of numerous signaling molecules.
- Fc gamma R-mediated phagocytosis - Homo sapiens (human)
Phagocytosis plays an essential role in host-defense mechanisms through the uptake and destruction of infectious pathogens. Specialized cell types including macrophages, neutrophils, and monocytes take part in this process in higher organisms.
- Focal adhesion - Homo sapiens (human)
Cell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the cell-extracellular matrix contact points, specialized structures are formed and termed focal adhesions, where bundles of actin filaments are anchored to transmembrane receptors of the integrin family through a multi-molecular complex of junctional plaque proteins.
- Fructose and mannose metabolism - Homo sapiens (human)
This pathway illustrates the shared catabolic fates of both fructose and mannose. Fructose occurs naturally in foods as a free monosaccharide and as a component of the disaccharide sucrose.
- D-Glutamine and D-glutamate metabolism
Glutamine is normally considered to be a nonessential amino acid. However, recent studies have provided evidence that glutamine may become "conditionally essential" during inflammatory conditions such as infection and injury.
- Glutathione metabolism - Homo sapiens (human)
Glutathione (GSH) is a tripeptide that contains an unusual peptide linkage between the amine group of cysteine (which is attached by normal peptide linkage to a glycine) and the carboxyl group of the glutamate side-chain. It is an antioxidant, preventing damage to important cellular components caused by reactive oxygen species such as free radicals and peroxides.
- Glycerophospholipid metabolism - Homo sapiens (human)
Glycerol is the backbone of the fundamental phospholipids used as the self-assembling units of lipid membranes. It is interesting that both enantiomeric glycerol configurations appear in nature.
- GnRH signaling pathway - Homo sapiens (human)
Gonadotropin-releasing hormone (GnRH) secretion from the hypothalamus acts upon its receptor in the anterior pituitary to regulate the production and release of the gonadotropins, LH and FSH. The GnRHR is coupled to Gq/11 proteins to activate phospholipase C which transmits its signal to diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3).
- Hedgehog signaling pathway - Homo sapiens (human)
The Hedgehog (Hh) family of secreted signaling proteins plays a crucial role in development of diverse animal phyla, from Drosophila to humans, regulating morphogenesis of a variety of tissues and organs. Hh signaling is also involved in control of stem cell proliferation in adult tissues and aberrant activation of the Hh pathway has been linked to multiple types of human cancer.
- Hexosamine signaling pathway - Homo sapiens (human)
The hexosamine biosynthetic pathway (HBP) results in the production of UDP-N-acetylglucosamine (UDP-GlcNAc) and other nucleotide hexosamines. UDP-GlcNAc, the major product, is the unique donor for the O-linkage of a single N-acetylglucosamine molecule (O-GlcNAc) to many cytoplasmic and nuclear proteins.
- Hormesis and adaptive cellular stress response pathways
Hormesis (from Greek hórmēsis "rapid motion, eagerness," from ancient Greek hormáein "to set in motion, impel, urge on") is the term for generally favorable biological responses to low exposures to toxins and other stressors. A pollutant or toxin showing hormesis thus has the opposite effect in small doses as in large doses. A related concept is Mithridatism, which refers to the willful exposure to toxins in an attempt to develop immunity against them. Hormetics is the term proposed for the study and science of hormesis. In toxicology, hormesis is a dose response phenomenon characterized by a low dose stimulation, high dose inhibition, resulting in either a J-shaped or an inverted U-shaped dose response. Such environmental factors that would seem to produce positive responses have also been termed "eustress."
- Insulin signaling pathway - Homo sapiens (human)
Insulin binding to its receptor results in the tyrosine phosphorylation of insulin receptor substrates (IRS) by the insulin receptor tyrosine kinase (INSR). This allows association of IRSs with the regulatory subunit of phosphoinositide 3-kinase (PI3K).
- Jak-STAT signaling pathway - Homo sapiens (human)
The Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway is one of a handful of pleiotropic cascades used to transduce a multitude of signals for development and homeostasis in animals, from humans to flies. In mammals, the JAK/STAT pathway is the principal signaling mechanism for a wide array of cytokines and growth factors.
- Leukocyte transendothelial migration - Homo sapiens (human)
Leukocyte migaration from the blood into tissues is vital for immune surveillance and inflammation. During this diapedesis of leukocytes, the leukocytes bind to endothelial cell adhesion molecules (CAM) and then migrate across the vascular endothelium.
- Linoleic acid metabolism - Homo sapiens (human)
Linoleic acid (LA) is a polyunsaturated fatty acid used in the biosynthesis of arachidonic acid (AA) and thus some prostaglandins. It is found in the lipids of cell membranes.
- The mitogen-activated protein kinase (MAPK) cascade
The mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals express at least four distinctly regulated groups of MAPKs, extracellular signal-related kinases (ERK)-1/2, Jun amino-terminal kinases (JNK1/2/3), p38 proteins (p38alpha/beta/gamma/delta) and ERK5, that are activated by specific MAPKKs: MEK1/2 for ERK1/2, MKK3/6 for the p38, MKK4/7 (JNKK1/2) for the JNKs, and MEK5 for ERK5.
- MTOR signaling pathway - Homo sapiens (human)
The mammalian target of rapamycin (mTOR) is an atypical serine/threonine kinase that is present in two distinct complexes. mTOR complex 1 (mTORC1) is composed of mTOR, Raptor, GβL (mLST8), and Deptor and is partially inhibited by rapamycin.
- Mucin type O-Glycan biosynthesis - Homo sapiens (human)
O-glycans are a class of glycans that modify serine or threonine residues of proteins. Biosynthesis of O-glycans starts from the transfer of N-acetylgalactosamine (GalNAc) to serine or threonine.
- Neurotrophin signaling pathway - Homo sapiens (human)
Neurotrophins are a family of trophic factors involved in differentiation and survival of neural cells. The neurotrophin family consists of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT-3), and neurotrophin 4 (NT-4).
- N-Glycan biosynthesis - Homo sapiens (human)
N-glycans or asparagine-linked glycans are major constituents of glycoproteins in eukaryotes. N-glycans are covalently attached to asparagine with the consensus sequence of Asn-X-Ser/Thr by an N-glycosidic bond, GlcNAc b1- Asn.
- NF-kB Signaling Pathway - Homo sapiens (human)
NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) is a protein complex that controls the transcription of DNA. NF-κB is found in almost all animal cell types and is involved in cellular responses to stimuli such as stress, cytokines, free radicals, ultraviolet irradiation, oxidized LDL, and bacterial or viral antigens.
- NOD-like receptor signaling pathway - Homo sapiens (human)
Specific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains more than 20 members in mammals and plays a pivotal role in the recognition of intracellular ligands.
- Notch signaling pathway - Homo sapiens (human)
The Notch signaling pathway is an evolutionarily conserved, intercellular signaling mechanism essential for proper embryonic development in all metazoan organisms in the Animal kingdom. The Notch proteins (Notch1-Notch4 in vertebrates) are single-pass receptors that are activated by the Delta (or Delta-like) and Jagged/Serrate families of membrane-bound ligands.
- Nrf2 and oxidative stress-induced gene expression - Homo sapiens (human)
One of the rational and effective strategies for chemoprevention is the blockade of DNA damage caused by carcinogenic insult. This can be achieved either by reducing the formation of reactive carcinogenic species or stimulating their detoxification.
- Oocyte meiosis - Homo sapiens (human)
During meiosis, a single round of DNA replication is followed by two rounds of chromosome segregation, called meiosis I and meiosis II. At meiosis I, homologous chromosomes recombine and then segregate to opposite poles, while the sister chromatids segregate from each other at meoisis II.
- p53 signaling pathway - Homo sapiens (human)
p53 activation is induced by a number of stress signals, including DNA damage, oxidative stress and activated oncogenes. The p53 protein is employed as a transcriptional activator of p53-regulated genes.
- Pantothenate and CoA biosynthesis
Panthothenate (vitamin B5) is the precursor of coenzyme A and is the prosthetic group of acyl carrier protein (ACP). Its name is derived from the Greek pantothen meaning “from everywhere” and small quantities of pantothenic acid are found in nearly every foodstuff.
- Pentose phosphate pathway - Homo sapiens (human)
The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathway.
- Polyamine synthesis and recycling - Homo sapiens (human)
Because of the important interactions of polyamines, synthesis and recycling of polyamines are some of the most tightly controlled cellular processes. Polyamine synthesis and recycling.
- PPAR signaling pathway - Homo sapiens (human)
Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that are activated by fatty acids and their derivatives. PPAR has three subtypes (PPARalpha, beta/delta, and gamma) showing different expression patterns in vertebrates.
- Prostaglandin II Biosynthesis and Arachidonic Acid Metabolism: Home sapiens
Arachidonic acid is a polyunsaturated fatty acid that is present in the phospholipids (especially phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositides) of membranes of the body's cells, and is abundant in the brain, muscles, liver. In addition to being involved in cellular signaling as a lipid second messenger involved in the regulation of signaling enzymes arachidonic acid is a key inflammatory intermediate and can also act as a vasodilator.
- Proteolysis/ Ubiquitin Pathway
The Ubiquitin Proteasome Pathway (UPP) is the principal mechanism for protein catabolism in the mammalian cytosol and nucleus. Modulation of protein activities by ubiquitin-dependent modification regulates the turnover, degradation and function of many cellular proteins.
- PTEN Sensing Pathway
Phosphatase and tensin homolog (PTEN) is a protein that, in humans, is encoded by the PTEN gene. Mutations of this gene are a step in the development of many cancers.
- Renin-angiotensin system - Homo sapiens (human)
The renin-angiotensin system (RAS) or the renin-angiotensin-aldosterone system (RAAS) is a hormone system that regulates blood pressure and water (fluid) balance. When blood volume is low, juxtaglomerular cells in the kidneys secrete renin directly into circulation.
- Selenocompound metabolism - Homo sapiens (human)
A nonmetallic chemical element found in trace amounts in human body. Selenium primarily occurs in vivo as selenocompounds, mostly selenoproteins such as glutathione peroxidase and thioredoxin reductase (enzymes responsible for detoxification).
- Starch and sucrose metabolism - Homo sapiens (human)
Carbohydrates are a major component of the human diet, and include starch (amylose and amylopectin) and disaccharides such as sucrose, lactose, maltose and, in small amounts, trehalose. The digestion of starch begins with the action of amylase enzymes secreted in the saliva and small intestine, which convert it to maltotriose, maltose, limit dextrins, and some glucose.
- Steroid biosynthesis - Homo sapiens (human)
Steroidogenesis is the biological process by which steroids are generated from cholesterol and transformed into other steroids. Steroids include estrogen, cortisol, progesterone, and testosterone.
- Taurine and hypotaurine metabolism - Homo sapiens (human)
Taurine, or 2-aminoethanesulfonic acid, is an organic acid widely distributed in animal tissues. It is a major constituent of bile and can be found in the large intestine and accounts for approximately 0.
- TGF-beta signaling pathway - Homo sapiens (human)
The transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species ranging from worms and insects to mammals. A wide spectrum of cellular functions such as proliferation, apoptosis, differentiation and migration are regulated by TGF-beta family members.
- Thiamine metabolism - Homo sapiens [human]
Thiamin(e), also known as vitamin B1, is known to play a fundamental role in energy metabolism. It consists of a pyrimidine ring (2,5-dimethyl-6-aminopyrimidine) and a thiazolium ring (4-methyl-5-hydroxy ethyl thiazole) joined by a methylene bridge.
- Toll-like receptor signaling pathway - Homo sapiens (human)
Specific families of pattern recognition receptors are responsible for detecting microbial pathogens and generating innate immune responses. Toll-like receptors (TLRs) are membrane-bound receptors identified as homologs of Toll in Drosophila.
- Tyrosine metabolism - Homo sapiens (human)
Tyrosine is found in many high protein food products such as soy products, chicken, turkey, fish, peanuts, almonds, avocados, bananas, milk, cheese, yogurt, cottage cheese, lima beans, pumpkin seeds, and sesame seeds. Tyrosine can be converted into L-DOPA, which is further converted into dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline).
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- Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human)
Ubiquinone (UQ), also called coenzyme Q, and plastoquinone (PQ) are electron carriers in oxidative phosphorylation and photosynthesis, respectively. The quinoid nucleus of ubiquinone is derived from the shikimate pathway; 4-hydroxybenzoate is directly formed from chorismate in bacteria, while it can be formed from either chorismate or tyrosine in yeast.
- VEGF signaling pathway - Homo sapiens (human)
There is now much evidence that VEGFR-2 is the major mediator of VEGF-driven responses in endothelial cells and it is considered to be a crucial signal transducer in both physiologic and pathologic angiogenesis. The binding of VEGF to VEGFR-2 leads to a cascade of different signaling pathways, resulting in the up-regulation of genes involved in mediating the proliferation and migration of endothelial cells and promoting their survival and vascular permeability.
- Vitamin B6 metabolism - Homo sapiens (human)
Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group. Several forms of the vitamin are known, but pyridoxal phosphate (PLP) is the active form and is a cofactor in many reactions of amino acid metabolism, including transamination, deamination, and decarboxylation.
- Transcription Role of Vitamin D Receptor: Homo sapiens (human)
Osteoporosis is a common disease affecting the majority of older women and a significant minority of older men. It is defined as the gradual reduction in bone strength with advancing age, particularly in post-menopause women.
- Warburg Effect
In oncology, the Warburg effect is the observation that most cancer cells predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol, rather than by a comparatively low rate of glycolysis followed by oxidation of pyruvate in mitochondria like most normal cells. Lactate production is typically restricted to anaerobic conditions when oxygen levels are low, however, cancer cells preferentially channel glucose towards lactate production even when oxygen is plentiful, a process termed 'aerobic gycolysis' or the Warburg Effect.
- Wnt signaling pathway - Homo sapiens (human)
Wnt proteins are secreted morphogens that are required for basic developmental processes, such as cell-fate specification, progenitor-cell proliferation and the control of asymmetric cell division, in many different species and organs. There are at least three different Wnt pathways: the canonical pathway, the planar cell polarity (PCP) pathway and the Wnt/Ca2+ pathway.
- Xenobiotic Detoxification Pathways: Acetaminophen, Dichloroethylene and Benzo[a]pyrene
Acetaminophen is bioactivated by the enzymes of the Cytochrome P450 family. It is oxidized via two pathways to form a toxic intermediate N-acetyl-1,4-benzoquinone imine believed to be responsible for the hepatotoxicity of Acetaminophen, and a nontoxic catechol metabolite 3-Hydroxy-acetaminophen.