Module #70, TG: 2.6, TC: 2.2, 103 probes, 100 Entrez genes, 4 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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metabolic process

The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

adaptive immune response

An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).

immune effector process

Any process of the immune system that occurs as part of an immune response.

activation of immune response

Any process that initiates an immune response.

immune system process

Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.

leukocyte mediated immunity

Any process involved in the carrying out of an immune response by a leukocyte.

lymphocyte mediated immunity

Any process involved in the carrying out of an immune response by a lymphocyte.

humoral immune response mediated by circulating immunoglobulin

An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.

adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains

An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus.

acute inflammatory response

Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.

activation of plasma proteins involved in acute inflammatory response

Any process activating plasma proteins by proteolysis as part of an acute inflammatory response.

regulation of immune system process

Any process that modulates the frequency, rate, or extent of an immune system process.

positive regulation of immune system process

Any process that activates or increases the frequency, rate, or extent of an immune system process.

defense response

Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.

complement activation

Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.

protein maturation by peptide bond cleavage

The hydrolysis of a peptide bond or bonds within a protein as part of protein maturation, the process leading to the attainment of the full functional capacity of a protein.

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).

inflammatory response

The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.

immune response

Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.

complement activation, alternative pathway

Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.

complement activation, classical pathway

Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.

humoral immune response

An immune response mediated through a body fluid.

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.

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.

gene expression

The process by which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.

immunoglobulin mediated immune response

An immune response mediated by immunoglobulins, whether cell-bound or in solution.

protein processing

Any protein maturation process achieved by the cleavage of peptide bonds.

protein metabolic process

The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.

B cell mediated immunity

Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells.

macromolecule metabolic process

The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.

primary metabolic process

The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.

innate immune response

Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

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.

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.

positive regulation of response to stimulus

Any process that activates, maintains or increases the rate 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.

regulation of immune response

Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

positive regulation of immune response

Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

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.

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.

protein maturation

Any process leading to the attainment of the full functional capacity of a protein.

biological regulation

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

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positive regulation of immune system process

Any process that activates or increases the frequency, rate, or extent of an immune system process.

regulation of immune system process

Any process that modulates the frequency, rate, or extent of an immune system process.

positive regulation of biological process

immune response

Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.

regulation of response to stimulus

positive regulation of response to stimulus

regulation of biological process

protein metabolic process

The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.

complement activation

positive regulation of immune system process

Any process that activates or increases the frequency, rate, or extent of an immune system process.

immune effector process

Any process of the immune system that occurs as part of an immune response.

regulation of immune response

Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

positive regulation of immune response

Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

positive regulation of immune response

Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

positive regulation of response to stimulus

regulation of immune response

Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

protein maturation

Any process leading to the attainment of the full functional capacity of a protein.

positive regulation of immune response

Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

activation of immune response

Any process that initiates an immune response.

complement activation

complement activation, alternative pathway

innate immune response

Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

inflammatory response

B cell mediated immunity

Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells.

complement activation, classical pathway

activation of plasma proteins involved in acute inflammatory response

Any process activating plasma proteins by proteolysis as part of an acute inflammatory response.

humoral immune response mediated by circulating immunoglobulin

An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.

complement activation

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.

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.

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.

pore complex

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

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.

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.

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.

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.

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.

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extracellular region part

cell part

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

membrane part

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.

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.

intrinsic to plasma membrane

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.

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.

binding

The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.

cell surface binding

Interacting selectively and non-covalently with any component on the surface of a cell.

bacterial cell surface binding

Interacting selectively and non-covalently with any component on the surface of a bacterial cell.

Gram-negative bacterial cell surface binding

Interacting selectively and non-covalently with any component on the surface of a Gram-negative bacterial cell.

all

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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.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0006952	1.381e-07	4.258	21	522	defense response
GO:0045087	7.246e-05	1.338	10	164	innate immune response
GO:0006954	9.622e-05	2.512	13	308	inflammatory response
GO:0006957	1.113e-04	0.08972	4 C8A, C8B, C9, CFP	11	complement activation, alternative pathway
GO:0006956	1.511e-04	0.2121	5 C8A, C8B, C9, CFP, MASP2	26	complement activation
GO:0002541	2.509e-04	0.2365	5 C8A, C8B, C9, CFP, MASP2	29	activation of plasma proteins involved in acute inflammatory response
GO:0002253	2.982e-04	0.6607	7 C8A, C8B, C9, CFP, LBP, MASP2, TRAT1	81	activation of immune response
GO:0006958	6.090e-04	0.1387	4 C8A, C8B, C9, MASP2	17	complement activation, classical pathway
GO:0009611	6.125e-04	4.029	15	494	response to wounding
GO:0051605	7.496e-04	0.5139	6 C8A, C8B, C9, CFP, LONP2, MASP2	63	protein maturation by peptide bond cleavage
GO:0006955	1.052e-03	4.25	15	521	immune response
GO:0002376	1.404e-03	6.68	19	819	immune system process
GO:0050896	1.457e-03	20.61	38	2527	response to stimulus
GO:0002526	2.119e-03	0.6362	6 C8A, C8B, C9, CFP, LBP, MASP2	78	acute inflammatory response
GO:0006950	2.513e-03	11.77	26	1443	response to stress
GO:0002455	2.726e-03	0.2121	4 C8A, C8B, C9, MASP2	26	humoral immune response mediated by circulating immunoglobulin
GO:0016485	2.993e-03	0.6851	6 C8A, C8B, C9, CFP, LONP2, MASP2	84	protein processing
GO:0050778	3.200e-03	1.011	7 C8A, C8B, C9, CFP, LBP, MASP2, TRAT1	124	positive regulation of immune response
GO:0051604	3.949e-03	0.7259	6 C8A, C8B, C9, CFP, LONP2, MASP2	89	protein maturation
GO:0006959	6.184e-03	0.5057	5 C8A, C8B, C9, CFP, MASP2	62	humoral immune response
GO:0050776	6.875e-03	1.566	8	192	regulation of immune response
GO:0006968	1.034e-02	0.3181	4 CD5L, CXCR2, LBP, TRAT1	39	cellular defense response
GO:0006725	1.057e-02	0.9054	6 CYP1A1, MOCOS, PEMT, PRHOXNB, TAT, XDH	111	cellular aromatic compound metabolic process
GO:0008203	1.327e-02	0.6199	5 AKR1D1, APOA4, APOF, SOAT2, TM7SF2	76	cholesterol metabolic process
GO:0002252	1.351e-02	1.346	7 C8A, C8B, C9, CFP, FOXP3, LBP, MASP2	165	immune effector process
GO:0019835	1.372e-02	0.1468	3 C8A, C8B, C9	18	cytolysis
GO:0016125	1.755e-02	0.6688	5 AKR1D1, APOA4, APOF, SOAT2, TM7SF2	82	sterol metabolic process
GO:0048584	1.765e-02	1.868	8	229	positive regulation of response to stimulus
GO:0051818	2.038e-02	0.04078	2 C9, CAMP	5	disruption of cells of other organism involved in symbiotic interaction
GO:0051883	2.038e-02	0.04078	2 C9, CAMP	5	killing of cells in other organism involved in symbiotic interaction
GO:0002449	2.149e-02	0.7096	5 C8A, C8B, C9, FOXP3, MASP2	87	lymphocyte mediated immunity
GO:0044403	2.305e-02	0.416	4 C9, CAMP, CD209, LBP	51	symbiosis, encompassing mutualism through parasitism
GO:0016064	2.544e-02	0.4323	4 C8A, C8B, C9, MASP2	53	immunoglobulin mediated immune response
GO:0002460	2.666e-02	0.7585	5 C8A, C8B, C9, FOXP3, MASP2	93	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0019724	2.679e-02	0.4404	4 C8A, C8B, C9, MASP2	54	B cell mediated immunity
GO:0002250	2.846e-02	0.7749	5 C8A, C8B, C9, FOXP3, MASP2	95	adaptive immune response
GO:0015721	3.413e-02	0.0571	2 AQP8, SLC10A1	7	bile acid and bile salt transport
GO:0043604	3.413e-02	0.0571	2 OTC, PRHOXNB	7	amide biosynthetic process
GO:0050710	3.413e-02	0.0571	2 FOXP3, NLRP12	7	negative regulation of cytokine secretion
GO:0002443	4.053e-02	0.8646	5 C8A, C8B, C9, FOXP3, MASP2	106	leukocyte mediated immunity
GO:0030299	4.201e-02	0.06525	2 APOA4, SOAT2	8	intestinal cholesterol absorption
GO:0034433	4.201e-02	0.06525	2 APOA4, SOAT2	8	steroid esterification
GO:0034434	4.201e-02	0.06525	2 APOA4, SOAT2	8	sterol esterification
GO:0034435	4.201e-02	0.06525	2 APOA4, SOAT2	8	cholesterol esterification
GO:0050746	4.201e-02	0.06525	2 APOA4, PEMT	8	regulation of lipoprotein metabolic process
GO:0002684	4.429e-02	1.77	7 C8A, C8B, C9, CFP, LBP, MASP2, TRAT1	217	positive regulation of immune system process

HELP

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.

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

Id	Pvalue	ExpCount	Count	Size	Term
GO:0005576	9.705e-09	11.69	36	1407	extracellular region
GO:0005579	4.384e-04	0.05815	3 C8A, C8B, C9	7	membrane attack complex
GO:0005615	8.543e-03	4.561	13	549	extracellular space
GO:0044421	1.410e-02	6.139	15	739	extracellular region part
GO:0042581	2.216e-02	0.06646	2 CAMP, CRISP3	8	specific granule
GO:0044432	3.727e-02	4.27	11	514	endoplasmic reticulum part
GO:0071212	4.962e-02	4.478	11	539	subsynaptic reticulum
GO:0034364	4.996e-02	0.108	2 APOA4, APOF	13	high-density lipoprotein particle

HELP

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.

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

Id	Pvalue	ExpCount	Count	Size	Term
GO:0051636	6.091e-03	0.02357	2 LBP, STAB2	3	Gram-negative bacterial cell surface binding
GO:0061134	1.517e-02	1.029	6	131	peptidase regulator activity
GO:0030151	1.592e-02	0.03929	2 MOCOS, XDH	5	molybdenum ion binding
GO:0008289	2.193e-02	2.522	9	321	lipid binding
GO:0004866	2.810e-02	0.8094	5	103	endopeptidase inhibitor activity
GO:0061135	3.078e-02	0.833	5	106	endopeptidase regulator activity
GO:0030414	3.281e-02	0.8487	5	108	peptidase inhibitor activity
GO:0043498	3.896e-02	0.2515	3 APOA4, LBP, STAB2	32	cell surface binding

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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.

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

Id	Pvalue	ExpCount	Count	Size	Term
00140	2.411e-02	0.2179	3 AKR1D1, CYP1A1, CYP3A43	22	Steroid hormone biosynthesis
04610	2.647e-02	0.4953	4 C8A, C8B, C9, MASP2	50	Complement and coagulation cascades
05020	2.939e-02	0.2377	3 C8A, C8B, C9	24	Prion diseases
00830	3.211e-02	0.2477	3 CYP1A1, CYP3A43, RDH16	25	Retinol metabolism

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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.

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

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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
ppy_lv_f_ca1	ppy	lv	f	_
ppy_lv_m_ca1	ppy	lv	m	_
mml_lv_f_ca1	mml	lv	f	_
mml_lv_m_ca1	mml	lv	m	_

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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 — 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 KEGG Pathway 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

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