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Current contents


Current release of the GeneNet contains 39 gene network diagrams.


Gene network diagrams

Diagram name Description Species Expert(s)
Cell cycle
Cell Cycle (G0/G1-S transition) Gene network of cell cycle regulationin in vertebrata (G0/G1-S transition).The diagram includes: transduction pathways for mitogenic and antimitogenic signals. The key transcription factor is E2F/DP Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Turn
Cell cycle (fission yeast) The gene network of a control of cell cycle in fission yeast. Saccharomyces pombe (fission yeast) Turn
Apoptosis (general scheme) Apoptosis occurs normally during the development of multicellular organisms  though a genetically regulated program or during the immune response when unwanted or infected cells are selectively removed. In addition, the apoptosis program can be activated in response to stress conditions, including heat shock, radiation, hypoxia, oxidants, ethanol and heavy metals. In extreme cases of stress, such as under conditions of intracellular ATP depletion   or at extremely high level of free radicals cells die by Necrosis. Bos taurus (bovine)
Homo sapiens (human)
Rattus norvegicus (rat)
Mus musculus (mouse)
Stepanenko I.L.
Immune response
Antiviral response IFN signal transduction pathways Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Ananko E.
JAK/STAT signal transduction pathway Subschema " JAK/STAT signal transduction pathway" for the scheme "Antiviral response" Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Ananko E.
Macrophage activation (model) Macrophage activation: the core of the mathematical model Gallus gallus (chicken)
Homo sapiens (human)
Rattus norvegicus (rat)
Mus musculus (mouse)
Nedosekina E.A.
NO biosynthesis pathway Pathway of NO biosynthesis induced by lipopolisaccharides (LPS) and interferons (IFN) Gallus gallus (chicken)
Homo sapiens (human)
Rattus norvegicus (rat)
Mus musculus (mouse)
Nedosekina E.A.
MAPK cascade Mitogen-activated protein kinase (MAPK) cascade initiated by lipopolisaccarides (LPS), macrophage colony-stimulating factor (CSF)-1, interferon(IFN)-gamma and tumor necrosis factor(TNF)-alpha. The cascade result in activation of transcription factors such as: Elk-1, ATF-2, NF-IL6, SAP-1alpha and c-Jun. Homo sapiens (human)
Mus musculus (mouse)
Nedosekina E.A.
NF-kappaB activation NF-kappaB proteins are present in the cytoplasm in association with inhibitory proteins. After activation by a large number of inducers, the IkappaB become phosphorylated, ubiquitylated and degraded by the proteasome. The degradation of IkappaB allows NF-kappaB to translocate to the nucleus and bind their DNA binding sites to regulate the transcription of a large number of genes, including antimicrobial peptides, cytokines, chemokines, stress-response proteins and anti-apoptosis proteins. Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Stepanenko I.L.
Lipid metabolism
Adipocyte Gene network includes experimental information on the mechanisms of gene expression regulation in adipocytes, as well as on the data on five biochemical pathways: i) input and utilization of glucose; ii) input and utilization of fatty acids; iii) biosynthesis of fatty acids; iv) biosynthesis of triglycerids; v) biosynthesis of cholesterol. Cricetulus griseus (hamster)
Homo sapiens (human)
Mesocricetus auratus (Syrian hamster) 
Mus musculus (mouse)
Rattus norvegicus (rat)
Ignatieva E.V.

Proscura A.L.

Cholesterol Intracellular regulation of cholesterol homeostasis. Factors of SREBP subfamily are the central link of this gene network. They are activated by the sterol-regulated proteases (SRP), which are suppressed by high concentrations of cholesterol. The genes, regulated by SREBP encode the enzymes of cholesterol biosynthesis and the LDL receptor that mediates supply of lipids (including cholesterol) into the cell. Cricetulus griseus (hamster)
Homo sapiens (human)
Mesocricetus auratus (Syrian hamster)
Rattus norvegicus (rat)
Ignatieva E.V.
Cholesterol_MODEL The mathematical model on intracellular cholesterol level regulation is based on the data from this diagram. Cricetulus griseus (hamster)
Homo sapiens (human)
Mesocricetus auratus (Syrian hamster)
Rattus norvegicus (rat)
Ignatieva E.V.
Cholesterol metabolism (intracellular)

Gene network includes information on: intracellular regulation of cholesterol homeostasis:
a) biosynthesis of cholesterol;
b) receptor mediated uptake of lipoproteins into the cell;
c) regulation of gene expression by transcription factors SREBPs, activated by the sterol-regulated protease (SRP).

Cricetulus griseus (hamster)
Homo sapiens (human)
Mesocricetus auratus (Syrian hamster)
Mus musculus (mouse)
Rattus norvegicus (rat)
Ignatieva E.V.
Leptin (organism level) This diagram accumulates experimental data concerning the body weight regulation. The scheme unites data obtained experimentally using several organisms (mouse, rat and human). The genes involved into the interactions described are expressed in the cells of different tissues and organs. The coordinated expression is regulated through signal substances (hormones, releasing factors and neurotransmitters). The central link of the regulation is leptin, secreted by adipose cells. Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Ignatieva E.V.
Lipid metabolism in blood

Gene network includes information on:
a) transport of dietary triglyceride and cholesterol (chilomicron metabolism);
b) transport of endogenous triglyceride and cholesterol (metabolism of VLDL);
c) reverse cholesterol transport.

 
Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Oryctolagus cuniculus (rabbit)
Rattus norvegicus (rat)
Proscura A.L.
Lipid metabolism in liver cells

Gene network includes experimental information on the mechanisms of gene expression regulation in liver cells. The diagram includes data on several biochemical pathways:
a) input and utilization of glucose;
b) input and utilization of fatty acids;
c) biosynthesis of fatty acids;
d) biosynthesis of triglycerids;
e) biosynthesis of cholesterol;
f) bile acids biosynthesis;
g) biosynthesis of lipoproteins

Cricetulus griseus (Cricetulus griseus)
Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Proscura A.L.
Endocrine system
Principal cell of CCD Principal cell of Cortical Collecting Duct This diagram represents two-step model of aldosterone action on Na+,K+-ATPase function in the principal cells of kidney cortical collecting duct (CCD). One is the classical genomic way of aldosterone action, so called long term action. It takes hours and days. This signal pathway is realized through the interaction with the mineralocorticoid receptors situated in the cytoplasm. The second is nongenomic way of aldosterone action. This way takes seconds and minutes. It is realized through the membrane receptor that stimulates activity of phospholipase C. Aldosterone could act through both mechanisms simultaneously, and these mechanisms appear to be important co-mediators of the wide range of cellular steroid effects. Rattus norvegicus (rat) Ignatieva E.V.

Logvinenko N.S.

Steroidogenesis (adrenal cortex) The scheme of glucocorticoid and mineralocorticoid hormones biosynthesis and its transcription regulation.
The scheme represents data on the transcription factors regulating expression of genes, encoding basic enzymes of steroid hormone synthesis in adrenal cortex, where glucocorticoids and mineralocorticoids are synthesized. The model is constructed on the basis of the information, accumulated in TRRD about regulation of transcription of the genes of various species of vertebrates.
Bos taurus (bovine (cattle)
Homo sapiens (human)
Mus musculus (mouse)
Ovis aries (sheep)
Rattus norvegicus (rat)
Busygina T.V.
Steroidogenesis (sex steroids) The scheme of sex steroid hormones biosynthesis and its transcription regulation.
The scheme represents data on the transcription factors regulating expression of genes, encoding basic enzymes of sex steroids biosynthesis, which are synthesized mainly in male and female gonads. The model is constructed on the basis of the information, accumulated in TRRD about regulation of transcription of the genes of various species of vertebrates.
Bos taurus (bovine (cattle)
Homo sapiens (human)
Mus musculus (mouse)
Ovis aries (sheep)
Rattus norvegicus (rat)
Busygina T.V.
Thyroid system Molecular bases of thyroid system endocrine regulation. The fragment of a gene network dealing with hypothalamic, hypophysial, and thyroidal interactions, controlling the thyroid hormone biosynthesis. Canis familiaris (dog)
Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Rattus rattus (black rat)
Suslov V.V.
Erythroid differentiation
Erythroid differentiation The processes occurring in erythroid cell differentiating under the action of erythropoietin. Transcription factor GATA-1 is the key link of this gene network. Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Podkolodnaya O.A.
Plant gene networks
Germination (endosperm) Germination process is under environmental control. Humidity, temperature, light regime, etc. form the optimal conditions triggering the ontogenesis. Hordeum vulgare (barley)
Oryza sativa (rice)
Prunus amygdalus (almond)
Triticum aestivum (wheat)
Zea mays (maize)
Tana

Alex

LEA program Gene network on preparation of a seed to a dormancy period. The key regulator of the second gene network, which inhibits premature vivipary of seeds and induces the most part of the known LEA genes, is a phytohormone ABA, abscisic acid. The product of the Vp1 gene mediates the signal transduction. The exact mechanism of seed dehydration is unknown to date. Positive feedback stimulates the process. As the result of the gene net functioning, a dehydration of seeds takes place, which in its turn induces the genes of late embryogenesis and the products of these genes provide further dehydration. Arabidopsis thaliana (mouse ear-cress)
Avena fatua (oat)
Brassica napus (oilseed rape)
Glycine max (soybean)
Hordeum vulgare (barley)
Oryza sativa (rice)
Phaseolus vulgaris (bean)
Pisum sativum (pea)
Prunus amygdalus (almond)
Sorghum bicolor (sorghum)
Triticum aestivum (wheat)
Vicia faba (fava bean)
Zea mays (maize)
Tana

Stepanenko I.L.

Nodulation This gene network involves coordinated expression of genes of two different organisms. Flavonoids secreted by plant roots induce transcription of the nodD gene in nitrogen-fixing bacteria (Rhizobium, Bradyrhizobium, and Azorhizobium). Its protein product, NodD, acts as a transcription activator of the other bacterial nod genes which are involved in synthesis of the Nod factor, a signal lipooligosaccharide. The factor stimulates differentiation of epidermal cells and induces expression of early nodulins and the cell-cycle genes in plants. This results in formation of a nodule, in which nitrogen fixation occurs. Arabidopsis thaliana (mouse ear-cress)
Glycine max (soybean)
Hordeum vulgare (barley)
Lupinus angustifolius (narrow-leaved blue lupine)
Lycopersicon esculentum (tomato)
Medicago sativa (alfalfa)
Medicago truncatula (barrel medic)
Nicotiana tabacum (common tobacco)
Petroselinum crispum (parsley)
Phaseolus vulgaris (French bean)
Pisum sativum (pea)
Rhizobium sp. (Rhizobium sp.)
Sesbania rostrata (sesbania)
Vicia faba (fava bean)
Vicia sativa (spring vetch)
Zea mays (maize)

Ibragimova S.S.

Stepanenko I.L.

Photomorphogenesis

Light is a critical environmental signal that effects seedling morphogenesis. A complex network of photoreceptors and signaling pathways have evolved to regulate expression of an enormous number of genes to light quantity, quality and duration.

Arabidopsis thaliana (mouse ear-cress)
Avena sativa (oat)
Glycine max (soybean)
Lycopersicon esculentum (tomato)
Nicotiana plumbaginifolia (curled-leaved tobacco)
Oryza sativa (rice)
Petroselinum crispum (parsley)
Pisum sativum (pea)
Sinapis alba (white mustard)

Smirnova O.G.

Stepanenko I.L.

Plant-pathogen Higher plants are equipped with a set of mechanisms protecting them from diseases caused by pathogen bacteria, fungi or viruses. During the contact between plant and pathogenic microorganism, a particular chain of events is produced in the plant organism. The interaction between plant and pathogen may develop by two ways given below.
1. The plant is provided by a receptor that interacts with bacterial protein. As a result, quick protective reaction is being developed. In such a situation, the bacteria is called avirulent for a given plant genotype [Piffanelli P. et al., 1999, Martin G.B., 1999].
2. The proteins of the pathogenic organism are virulent for the given plant genotype. The plant is affected by the pathogen, whereas protective mechanisms are being activated more slowly [Maleck K and Lawton K., 1998].
In both cases, with the start of pathogenesis gene transcription, the cell walls strengthen. Then in the place of pathogen penetration, the active forms of oxygen are formed, causing the death of infected cells.
Arabidopsis thaliana (mouse ear-cress)
Catharanthus roseus (periwinkle)
Cladosporium fulvum (cladosporium)
Hordeum vulgare (barley)
Linum usitatissimum (flax)
Lycopersicon esculentum (tomato)
Nicotiana sylvestris (tobacco)
Nicotiana tobacum (tobacco)
Oryza sativa (rice)
Petroselinum crispum (parsley)
Phaseolus vulgaris (bean)
Pseudomonas syringae (Pseudomonas syringae pv. tomato)
Pseudomonas syringae pv. maculicola (Pseudomonas syringae pv. maculicola)
Tana
Seed reserve mobilisation (1): carbohydrates This diagramm is the part of the gene network "Seed reserve mobilisation ". It involved with the mobilisation of carbohydrates during a germination of all seed types. Hordeum vulgare (barley)
Zea mays (maize)
Tana

Alex

Seed reserve mobilisation (2): lipids and phosphates The diagram is the part of the gene network "Seed reserve mobilisation" involved with lipids and phosphates mobilisation during a germination of all seed types. Hordeum vulgare (barley)
Triticum aestivum (wheat)
Tana

Alex

Seed reserve mobilisation (3): proteins This diagram shows the part of the gene network "Seed reserve mobilisation" involved with protein mobilisation during a germination of all seed types. Hordeum vulgare (barley) Tana

Alex

Seed reserve mobilisation (4): regulatory relationships The diagram of regulatory relationships between elements of the gene network involved with the seed reserve mobilisation during a germination of all seed types Hordeum vulgare (barley)
Triticum aestivum (wheat)
Zea mays (maize)
Tana

Alex

Seed reserve mobilisation (5): the general diagram The general diagram of the gene network "Seed reserve mobilisation" shows genes, enzymes, substances, compartments, and relationships , which acts during germination of all seed types to supply a growing embryo with energy and structure molecules from seed reserves. Hordeum vulgare (barley)
Triticum aestivum (wheat)
Zea mays (maize)
Tana

Alex

Seed reserve mobilisation (organism level) Expression of hydrolases during germination. Hormonal regulation. Hordeum vulgare (barley)
Triticum aestivum (wheat)
Zea mays (maize)
Tana

Alex

Storage protein biosynthesis (dicot) Among obligatory stages of seed maturation are accumulation and packaging of storages that will be necessary for germinating embryo.
DE At the initial stage, a considerable increase of a seed in size takes place, mainly due to the storage tissues growth.
Glycine max (soybean)
Phaseolus vulgaris (bean)
Pisum sativum (pea)
Prunus amygdalus (almond)
Vicia faba (fava bean)
Tana

Alex

Storage protein biosynthesis (monocot) Monocot seed storage protein genes expression is limited to endosperm tissues and occurs exclusively in a period of seed maturation. Coix lacryma-jobi (Job's tears)
Hordeum vulgare (barley)
Oryza sativa (rice)
Sorghum bicolor (sorghum)
Triticum aestivum (wheat)
Zea mays (maize)
Tana

Alex

REDOX-regulation
REDOX-REGULATION Activity of a number of transcription factors is post-translationally altered by redox modifications of specific cysteine residues. Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Saccharomyces cerevisiae (baker's yeast)
Stepanenko I.L.
Oxidative stress response (glutathione) Glutathione is involved into many cell processes, from antioxidant protection to proliferation modulation because of redox regulation function in cells. Acting as a buffer system, the ratio of two forms of glutathione maintains a redox potential in different cell compartments at a certain level. This gene network provides a response of glutathione homeostasis to hydrogen peroxide exposure. Prospects of modeling this gene network is a direct approach to the problem of drug resistance of cancer cell lines, which is related to increased activity of glutathione transferases, active transport of glutathione conjugates and drugs, and glutathione synthesis. Gallus gallus (chicken)
Homo sapiens (human) 
Rattus norvegicus (rat) 
Mus musculus (mouse)
Stepanenko I.L.
Heat Shock Response
HSP70 autoregulation Activation of HSF1 transcription factor is linked to the appearance of nonnative proteins. Upon heat shock or other forms of stress HSF1 assembles into active trimer, binds to HSE in hsp70 promoter and becomes hyperphosphorylated. A high level of HSP70 and HSP90 facilitates dissociation of HSF1 from HSE and dephosphorylation of HSF1 during recovery from heat shock. Homo sapiens (human)
Mus musculus (mouse)
Rattus norvegicus (rat)
Stepanenko I.L.
Heat Shock Response Every cell responds to environmental, chemical, and physiological stress through a rapid and preferential increase in expression of a highly conserved group of proteins known as the heat shock proteins (HSP). The HSPs protect the cells from various stresses and can be grouped into three general classes: chaperones that act in refolding of misfolded proteins, proteases that degrade of damaged proteins and stress-specific proteins alleviating specific stress. Drosophila melanogaster (Drosophila)
Gallus gallus (chicken)
Homo sapiens (human)
Hydra oligactis (hydra)
Mus musculus (mouse)
Rattus norvegicus (rat)
Saccharomyces cerevisiae (baker's yeast)
Saccharomyces pombe (fission yeast)
Sus scrofa (pig)
Xenopus laevis (African clawed frog)
Stepanenko I.L.
Thermotolerance Cells can respond to stress by adaptive changes that increase their ability  to tolerate normally lethal conditions. The cellular stress response   can mediate cellular protection through expression of heat-shock protein,   which can interfere with the process of apoptotic cell death. The protection   of cells from stress-induced apoptosis by the heat shock protein Hsp70   involves suppression of stress kinase JNK. Stress-induced apoptosis proceeds   through a defined biochemical process that involves cytochrome C, Apaf-1 and caspase. Hsp70, HSP27 and HSP90 prevent cytochrome c-mediated caspase  activation and suppresses apoptosis by directly associating with Apaf-1 and blocking the assembly of a functional apoptosome. Homo sapiens (human)
Rattus norvegicus (rat)
Stepanenko I.L.

 

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