Module #100, TG: 2.8, TC: 2.4, 30 probes, 30 Entrez genes, 10 conditions

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Under-expression is coded with green, over-expression with red color.

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This is one of three sections showing Gene Ontology enrichment of the current module: in this case for biological processes.

The graph shows the hierarchy of the GO categories, their enrichment for the current module is color coded, and the blue number beside the category is the minus log ten p-value of the enrichment. (Calculated using the standard hypergeometric test.) The color of the arrows code «is a» (cyan) and «part of» relationships.

The tree was built the following way. First all GO terms with more significant enrichment p-value than 0.05 were collected. Then all paths from these terms to the root node of the GO tree were included too. If a GO term is included more than once in the tree, then the green numbers show 1) the id of the node, this makes it easier to find other appereances of the term, and 2) the number of appearences.

Note that the same GO category might show up on the graph many times. This is because the GO was «straightened» for this graph, i.e. if there are more paths from a GO term to the root node of the tree, all of them are included. The green numbers

Move the mouse cursor over the terms to get their definition. Clicking on them takes you to the corresponding Gene Ontology web page.

If you cannot see a graph here at all, that means that there were no significantly enriched GO categories, at the 0.05 level.

— Click on the Help button again to close this help window.

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cell activation

A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.

blood coagulation

The sequential process by which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.

response to stress

A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

growth

The increase in size or mass of an entire organism, a part of an organism or a cell.

multicellular organismal development

The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

anatomical structure morphogenesis

The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.

tissue development

The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.

hemostasis

The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.

biological_process

Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

negative regulation of coagulation

Any process that stops, prevents or reduces the frequency, rate or extent of coagulation.

response to external stimulus

A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.

response to wounding

A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.

cellular process

Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

platelet activation

A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.

regulation of blood coagulation

Any process that modulates the frequency, rate or extent of blood coagulation.

positive regulation of blood coagulation

Any process that activates or increases the frequency, rate or extent of blood coagulation.

negative regulation of blood coagulation

Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation.

regeneration

The regrowth of a lost or destroyed body part, such as an organ or tissue.

regulation of response to external stimulus

Any process that modulates the frequency, rate or extent of a response to an external stimulus.

multicellular organismal process

Any biological process, occurring at the level of a multicellular organism, pertinent to its function.

developmental process

A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.

wound healing

The series of events that restore integrity to a damaged tissue, following an injury.

tissue regeneration

The regrowth of lost or destroyed tissues.

fibrinolysis

An ongoing process that solubilizes fibrin, chiefly by the proteolytic action of plasmin, resulting in the removal of small blood clots.

organ development

Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.

positive regulation of biological process

Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

negative regulation of biological process

Any process that stops, prevents or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

regulation of response to stimulus

Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

developmental growth

The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.

system development

The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.

anatomical structure development

The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.

regulation of biological process

Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

coagulation

The process by which a fluid solution, or part of it, changes into a solid or semisolid mass.

regulation of coagulation

Any process that modulates the frequency, rate or extent of coagulation, the process by which a fluid solution, or part of it, changes into a solid or semisolid mass.

positive regulation of coagulation

Any process that activates or increases the frequency, rate or extent of coagulation.

regulation of body fluid levels

Any process that modulates the levels of body fluids.

response to stimulus

A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.

regulation of multicellular organismal process

Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.

positive regulation of multicellular organismal process

Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.

negative regulation of multicellular organismal process

Any process that stops, prevents or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.

regulation of fibrinolysis

Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.

negative regulation of fibrinolysis

Any process that stops, prevents or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.

regulation of wound healing

Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.

biological regulation

Any process that modulates the frequency, rate or extent of any biological process, quality or function.

regulation of biological quality

Any process that modulates the frequency, rate or extent of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.

regulation of response to stress

Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

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multicellular organismal development

developmental growth

positive regulation of multicellular organismal process

negative regulation of multicellular organismal process

positive regulation of biological process

negative regulation of biological process

regulation of multicellular organismal process

regulation of response to stimulus

regulation of biological process

regulation of coagulation

Any process that modulates the frequency, rate or extent of coagulation, the process by which a fluid solution, or part of it, changes into a solid or semisolid mass.

positive regulation of multicellular organismal process

negative regulation of multicellular organismal process

positive regulation of coagulation

Any process that activates or increases the frequency, rate or extent of coagulation.

negative regulation of coagulation

Any process that stops, prevents or reduces the frequency, rate or extent of coagulation.

anatomical structure morphogenesis

The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.

system development

negative regulation of fibrinolysis

Any process that stops, prevents or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.

regulation of response to stress

regulation of response to external stimulus

Any process that modulates the frequency, rate or extent of a response to an external stimulus.

regulation of body fluid levels

Any process that modulates the levels of body fluids.

organ development

platelet activation

negative regulation of blood coagulation

Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation.

negative regulation of coagulation

Any process that stops, prevents or reduces the frequency, rate or extent of coagulation.

regulation of blood coagulation

Any process that modulates the frequency, rate or extent of blood coagulation.

positive regulation of coagulation

Any process that activates or increases the frequency, rate or extent of coagulation.

positive regulation of blood coagulation

Any process that activates or increases the frequency, rate or extent of blood coagulation.

blood coagulation

tissue regeneration

The regrowth of lost or destroyed tissues.

tissue regeneration

The regrowth of lost or destroyed tissues.

tissue development

The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.

regulation of blood coagulation

Any process that modulates the frequency, rate or extent of blood coagulation.

positive regulation of blood coagulation

Any process that activates or increases the frequency, rate or extent of blood coagulation.

negative regulation of blood coagulation

Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation.

negative regulation of fibrinolysis

Any process that stops, prevents or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.

regulation of blood coagulation

Any process that modulates the frequency, rate or extent of blood coagulation.

blood coagulation

tissue regeneration

The regrowth of lost or destroyed tissues.

regulation of wound healing

Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.

regulation of fibrinolysis

Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.

negative regulation of fibrinolysis

Any process that stops, prevents or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.

HELP

This is one of three sections showing Gene Ontology enrichment of the current module: in this case for cellular components.

Move the mouse cursor over the terms to get their definition. Clicking on them takes you to the corresponding Gene Ontology web page.

If you cannot see a graph here at all, that means that there were no significantly enriched GO categories, at the 0.05 level.

— Click on the Help button again to close this help window.

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plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

intracellular

The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

membrane

Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.

integral to membrane

Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane.

extracellular region

The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

integral to plasma membrane

Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer.

cellular_component

The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

fibrinogen complex

A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.

membrane attack complex

A protein complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow.

extracellular space

That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

cell

The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

stored secretory granule

A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

external side of plasma membrane

The side of the plasma membrane that is opposite to the side that faces the cytoplasm.

cell surface

The external part of the cell wall and/or plasma membrane.

pore complex

Any small opening in a membrane that allows the passage of gases and/or liquids.

cytoplasmic membrane-bounded vesicle

A membrane-bounded vesicle found in the cytoplasm of the cell.

platelet alpha granule

A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).

platelet alpha granule lumen

The volume enclosed by the membrane of the platelet alpha granule.

intrinsic to membrane

Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane.

intrinsic to plasma membrane

Located in the plasma membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane.

cytoplasmic vesicle

A vesicle formed of membrane or protein, found in the cytoplasm of a cell.

membrane-enclosed lumen

The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen.

vesicle

Any small, fluid-filled, spherical organelle enclosed by membrane or protein.

vesicle lumen

The volume enclosed by the membrane or protein that forms a vesicle.

membrane-bounded vesicle

Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer.

macromolecular complex

A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.

organelle

Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.

membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

intracellular organelle

Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

intracellular membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

organelle lumen

The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.

protein complex

Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.

extracellular region part

Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite.

organelle part

Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane.

intracellular part

Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

membrane part

Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.

cytoplasmic vesicle part

Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.

cytoplasmic part

Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

intracellular organelle part

A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.

plasma membrane part

Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

cell part

Any constituent part of a cell, the basic structural and functional unit of all organisms.

cytoplasmic membrane-bounded vesicle lumen

The volume enclosed by the membrane of a cytoplasmic membrane-bounded vesicle.

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extracellular region part

cell part

Any constituent part of a cell, the basic structural and functional unit of all organisms.

organelle part

organelle lumen

fibrinogen complex

cytoplasmic vesicle

A vesicle formed of membrane or protein, found in the cytoplasm of a cell.

intracellular membrane-bounded organelle

intracellular organelle part

fibrinogen complex

intracellular part

membrane part

intracellular organelle

intracellular organelle part

cytoplasmic vesicle part

Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.

cytoplasmic membrane-bounded vesicle

A membrane-bounded vesicle found in the cytoplasm of the cell.

vesicle lumen

The volume enclosed by the membrane or protein that forms a vesicle.

cytoplasmic membrane-bounded vesicle

A membrane-bounded vesicle found in the cytoplasm of the cell.

cytoplasmic membrane-bounded vesicle lumen

The volume enclosed by the membrane of a cytoplasmic membrane-bounded vesicle.

plasma membrane part

Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

cytoplasmic part

Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

cytoplasmic vesicle

A vesicle formed of membrane or protein, found in the cytoplasm of a cell.

cytoplasmic vesicle part

Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.

membrane attack complex

A protein complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow.

external side of plasma membrane

The side of the plasma membrane that is opposite to the side that faces the cytoplasm.

intrinsic to plasma membrane

cytoplasmic membrane-bounded vesicle lumen

The volume enclosed by the membrane of a cytoplasmic membrane-bounded vesicle.

pore complex

Any small opening in a membrane that allows the passage of gases and/or liquids.

integral to plasma membrane

Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer.

membrane attack complex

A protein complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow.

platelet alpha granule lumen

The volume enclosed by the membrane of the platelet alpha granule.

HELP

This is one of three sections showing Gene Ontology enrichment of the current module: in this case for molecular function.

Move the mouse cursor over the terms to get their definition. Clicking on them takes you to the corresponding Gene Ontology web page.

If you cannot see a graph here at all, that means that there were no significantly enriched GO categories, at the 0.05 level.

— Click on the Help button again to close this help window.

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molecular_function

Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.

enzyme inhibitor activity

Stops, prevents or reduces the activity of an enzyme.

endopeptidase inhibitor activity

Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.

serine-type endopeptidase inhibitor activity

Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.

endopeptidase regulator activity

Modulates the activity of a peptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.

peptidase inhibitor activity

Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.

enzyme regulator activity

Modulates the activity of an enzyme.

peptidase regulator activity

Modulates the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.

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peptidase inhibitor activity

Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.

endopeptidase inhibitor activity

Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.

HELP

List of all enriched GO categories (biological processes), at the 0.05 p-value level.

The columns:

ExpCount is the expected count of genes in the module annotated with the given GO term, just by chance.
Count is the number of genes in the module annotated with the given GO term.
Size is the total number of genes (in our universe) annotated with the GO term.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual GO category.

Clicking on the GO identifiers takes you to the Gene Ontology web pages.

— Click on the Help button again to close this help window.

Id	Pvalue	ExpCount	Count	Size	Term
GO:0042060	3.294e-08	0.5379	10	88	wound healing
GO:0009611	4.362e-08	1.29	13	211	response to wounding
GO:0006950	2.230e-06	3.765	17	616	response to stress
GO:0007596	3.930e-06	0.2995	7 CPB2, F2, F9, FGB, FGG, HRG, SERPINC1	49	blood coagulation
GO:0007599	4.468e-06	0.3056	7 CPB2, F2, F9, FGB, FGG, HRG, SERPINC1	50	hemostasis
GO:0050817	5.082e-06	0.3118	7 CPB2, F2, F9, FGB, FGG, HRG, SERPINC1	51	coagulation
GO:0050896	1.583e-05	6.473	20	1059	response to stimulus
GO:0050878	5.917e-05	0.4707	7 CPB2, F2, F9, FGB, FGG, HRG, SERPINC1	77	regulation of body fluid levels
GO:0051917	3.325e-04	0.03056	3 CPB2, F2, HRG	5	regulation of fibrinolysis
GO:0051918	3.325e-04	0.03056	3 CPB2, F2, HRG	5	negative regulation of fibrinolysis
GO:0030194	5.855e-04	0.03668	3 CPB2, F2, HRG	6	positive regulation of blood coagulation
GO:0042730	5.855e-04	0.03668	3 CPB2, F2, HRG	6	fibrinolysis
GO:0050820	1.365e-03	0.0489	3 CPB2, F2, HRG	8	positive regulation of coagulation
GO:0030195	2.490e-03	0.06113	3 CPB2, F2, HRG	10	negative regulation of blood coagulation
GO:0065008	2.687e-03	3.851	13	630	regulation of biological quality
GO:0050819	3.209e-03	0.06724	3 CPB2, F2, HRG	11	negative regulation of coagulation
GO:0030193	4.020e-03	0.07335	3 CPB2, F2, HRG	12	regulation of blood coagulation
GO:0030168	4.950e-03	0.07947	3 F2, FGB, FGG	13	platelet activation
GO:0042246	4.950e-03	0.07947	3 IGFBP1, SERPINA10, TM4SF4	13	tissue regeneration
GO:0061041	4.950e-03	0.07947	3 CPB2, F2, HRG	13	regulation of wound healing
GO:0031099	5.491e-03	0.2262	4 HGF, IGFBP1, SERPINA10, TM4SF4	37	regeneration
GO:0050818	7.077e-03	0.09169	3 CPB2, F2, HRG	15	regulation of coagulation
GO:0048583	7.251e-03	1.137	7 AMBP, C8A, C8B, CPB2, F2, HRG, SERPINC1	186	regulation of response to stimulus
GO:0006725	1.079e-02	0.2812	4 DBH, DHODH, TAT, TDO2	46	cellular aromatic compound metabolic process
GO:0051240	1.995e-02	0.6296	5 CPB2, DBH, F2, FST, HRG	103	positive regulation of multicellular organismal process
GO:0006957	2.082e-02	0.03056	2 C8A, C8B	5	complement activation, alternative pathway
GO:0042402	2.082e-02	0.03056	2 DBH, TDO2	5	cellular biogenic amine catabolic process
GO:0006955	2.696e-02	1.064	6 AMBP, C8A, C8B, DBH, IL18RAP, IL1R2	174	immune response
GO:0006958	2.785e-02	0.03668	2 C8A, C8B	6	complement activation, classical pathway
GO:0009074	2.785e-02	0.03668	2 TAT, TDO2	6	aromatic amino acid family catabolic process
GO:0019835	2.785e-02	0.03668	2 C8A, C8B	6	cytolysis
GO:0006954	2.809e-02	0.6969	5 C8A, C8B, F2, IL18RAP, SERPINC1	114	inflammatory response
GO:0080134	2.892e-02	0.703	5 AMBP, CPB2, F2, HRG, SERPINC1	115	regulation of response to stress
GO:0009063	3.052e-02	0.1712	3 DBH, TAT, TDO2	28	cellular amino acid catabolic process
GO:0009310	3.300e-02	0.1773	3 DBH, TAT, TDO2	29	amine catabolic process
GO:0042219	3.559e-02	0.04279	2 DBH, TDO2	7	cellular amino acid derivative catabolic process
GO:0051241	3.667e-02	0.4279	4 ABCG5, CPB2, F2, HRG	70	negative regulation of multicellular organismal process
GO:0032101	3.961e-02	0.4401	4 CPB2, F2, HRG, SERPINC1	72	regulation of response to external stimulus
GO:0002526	4.367e-02	0.2017	3 C8A, C8B, F2	33	acute inflammatory response
GO:0006956	4.367e-02	0.0489	2 C8A, C8B	8	complement activation
GO:0019439	4.367e-02	0.0489	2 TAT, TDO2	8	aromatic compound catabolic process
GO:0002443	4.650e-02	0.2078	3 C8A, C8B, DBH	34	leukocyte mediated immunity

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List of all enriched GO categories (cellular components), at the 0.05 p-value level.

The columns:

ExpCount is the expected count of genes in the module annotated with the given GO term, just by chance.
Count is the number of genes in the module annotated with the given GO term.
Size is the total number of genes (in our universe) annotated with the GO term.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual GO category.

Clicking on the GO identifiers takes you to the Gene Ontology web pages.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0005576	1.655e-08	3.253	18	533	extracellular region
GO:0031983	2.343e-06	0.09766	5 DBH, FGB, FGG, HGF, HRG	16	vesicle lumen
GO:0060205	2.343e-06	0.09766	5 DBH, FGB, FGG, HGF, HRG	16	cytoplasmic membrane-bounded vesicle lumen
GO:0005615	3.440e-06	1.379	11	226	extracellular space
GO:0044421	7.333e-05	1.953	11	320	extracellular region part
GO:0031093	7.943e-05	0.09156	4 FGB, FGG, HGF, HRG	15	platelet alpha granule lumen
GO:0031091	1.925e-04	0.116	4 FGB, FGG, HGF, HRG	19	platelet alpha granule
GO:0030141	6.279e-04	0.3357	5 DBH, FGB, FGG, HGF, HRG	55	stored secretory granule
GO:0009897	4.923e-03	0.2991	4 FGB, FGG, IL2RB, TRPM8	49	external side of plasma membrane
GO:0005579	5.282e-03	0.02442	2 C8A, C8B	4	membrane attack complex
GO:0005577	7.985e-03	0.03052	2 FGB, FGG	5	fibrinogen complex
GO:0044433	8.928e-03	0.6531	5 DBH, FGB, FGG, HGF, HRG	107	cytoplasmic vesicle part

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List of all enriched GO categories (molecular function), at the 0.05 p-value level.

The columns:

ExpCount is the expected count of genes in the module annotated with the given GO term, just by chance.
Count is the number of genes in the module annotated with the given GO term.
Size is the total number of genes (in our universe) annotated with the GO term.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual GO category.

Clicking on the GO identifiers takes you to the Gene Ontology web pages.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0004867	8.323e-04	0.1315	4 AMBP, HRG, SERPINA10, SERPINC1	23	serine-type endopeptidase inhibitor activity
GO:0004866	2.926e-03	0.1945	4 AMBP, HRG, SERPINA10, SERPINC1	34	endopeptidase inhibitor activity
GO:0061135	3.198e-03	0.2002	4 AMBP, HRG, SERPINA10, SERPINC1	35	endopeptidase regulator activity
GO:0030414	3.491e-03	0.2059	4 AMBP, HRG, SERPINA10, SERPINC1	36	peptidase inhibitor activity
GO:0061134	6.093e-03	0.2459	4 AMBP, HRG, SERPINA10, SERPINC1	43	peptidase regulator activity
GO:0043499	1.571e-02	0.0286	2 FGB, FGG	5	eukaryotic cell surface binding
GO:0004857	2.447e-02	0.3946	4 AMBP, HRG, SERPINA10, SERPINC1	69	enzyme inhibitor activity
GO:0004252	3.829e-02	0.2059	3 F2, F9, HGF	36	serine-type endopeptidase activity

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List of all enriched KEGG pathways, at the 0.05 p-value level.

The columns:

ExpCount is the expected count of genes in the module annotated with the given KEGG pathway, just by chance.
Count is the number of genes in the module annotated with the given KEGG pathway.
Size is the total number of genes (in our universe) annotated with the KEGG pathway.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual KEGG pathway.

Clicking on the KEGG identifiers takes you to the KEGG web site.

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Id	Pvalue	ExpCount	Count	Size	Term
04610	6.929e-09	0.2407	8	21	Complement and coagulation cascades

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List of all enriched miRNA families, at the 0.05 p-value level.

The columns:

ExpCount is the expected count of genes in the module regulated by the given miRNA family, just by chance.
Count is the number of genes in the module regulated by the given miRNA family.
Size is the total number of genes (in our universe) regulated with the given miRNA family.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual miRNA family.

The miRNA regulation data was taken from the TargetScan database. (Only the conserved sites were used for the current analysis.) Clicking on the miRNA names takes you to the TargetScan web site.

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List of all enriched Chromosomes, at the 0.05 p-value level.

The columns:

ExpCount is the expected number of genes in the module on the given chromosome, just by chance.
Count is the number of genes in the module on the given chromosome.
Size is the total number of genes (in our universe) on the given chromosome.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual chromosome.

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A list of all genes in the current module, in alphabetical order. The size of the text corresponds to the gene scores.

Text color indicates correlation and anti-correlation: genes of the same color are correlated, both move up or down in the module samples (listed below). Genes of different color are anti-correlated, they have opposite behavior in the module samples.

Note, that text color of the individual genes should be interpreted together with the coloring of the samples below. For red samples, red genes have a higher expression (compared to the average gene expression level), green genes have a lower expression.

Green samples have opposite behavior, in these red genes have a lower expression, green genes have a higher expression.

Note that some gene symbols may show up more than once, if many probes match the same Entrez gene.

Genes with no Entrez mapping are given separately, with their Affymetrics probe ID.

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Conditions in the module, given in the same order as on the expression plot above. Red color means over-expression, green under-expression in the given condition.

The barplot below shows the condition (sample) scores. A separate bar is shown for each sample, its height is the corresponding score of the sample in the module. The red and green numbers on the bars are the sample scores expressed in percents, i.e. 100% is 1.0.

The height of each bar corresponds to the weighted mean expression of the module genes. The weights are the gene scores of the module and they are positive for the genes listed in red above and they are negative for the genes that are listed in green.

Bars going up correspond to samples listed in red (the ones that are different enough to included in the module). In these samples the red module genes are highly expressed, and the green module genes are lowly expressed. The behavior of the genes is the opposite for bars going down.

The red and green lines show the module thresholds, samples above the red line and below the green line are included in the module.

The different species and tissues that were part of the study, are separated by dashed vertical lines.

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Id	species	tissue	sex	individual
ggo_lv_m_ca1	ggo	lv	m	_
ppa_lv_m_ca1	ppa	lv	m	_
ggo_lv_f_ca1	ggo	lv	f	_
ptr_lv_m_ca1	ptr	lv	m	_
mml_lv_m_ca1	mml	lv	m	_
hsa_lv_m1_ca1	hsa	lv	m	1
ppy_lv_m_ca1	ppy	lv	m	_
mml_lv_f_ca1	mml	lv	f	_
ppy_lv_f_ca1	ppy	lv	f	_
ppa_lv_f_ca1	ppa	lv	f	_

Previous module | Next module Module #100, TG: 2.8, TC: 2.4, 30 probes, 30 Entrez genes, 10 conditions

Help | Hide | Top Help | Show | Top Expression data

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Help | Hide | Top Help | Show | Top The GO tree — Biological processes

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Help | Hide | Top Help | Show | Top The GO tree — Cellular Components

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Help | Hide | Top Help | Show | Top The GO tree — Molecular Function

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Help | Hide | Top Help | Show | Top GO BP test for over-representation

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Help | Hide | Top Help | Show | Top GO CC test for over-representation

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Help | Hide | Top Help | Show | Top GO MF test for over-representation

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Help | Hide | Top Help | Show | Top KEGG Pathway test for over-representation

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Help | Hide | Top Help | Show | Top miRNA test for over-representation

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Help | Hide | Top Help | Show | Top Chromosome test for over-representation

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Help | Hide | Top Help | Show | Top Genes

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Entrez genes

Non-Entrez genes

Help | Hide | Top Help | Show | Top Conditions

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