Current release of the GeneNet contains 39 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. |
