Module #356, TG: 3.4, TC: 1.4, 21 probes, 21 Entrez genes, 17 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.

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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.

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.

monocyte chemotaxis

The movement of a monocyte in response to an external stimulus.

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.

cell motion

Any process involved in the controlled movement of a cell.

chemotaxis

The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).

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.

humoral immune response

An immune response mediated through a body fluid.

behavior

The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.

locomotory behavior

The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.

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 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.

cell migration

The orderly movement of cells from one site to another, often during the development of a multicellular organism or multicellular structure.

leukocyte chemotaxis

The movement of a leukocyte in response to an external stimulus.

locomotion

Self-propelled movement of a cell or organism from one location to another.

response to chemical 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 chemical stimulus.

taxis

The directed movement of a motile cell or organism in response to an external stimulus.

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.

cell motility

Any process involved in the controlled movement of a cell that results in translocation of the cell from one place to another.

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.

leukocyte migration

The movement of leukocytes within or between different tissues and organs of the body.

localization

Any process by which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location.

localization of cell

Any process by which a cell is transported to, and/or maintained in, a specific location.

cell chemotaxis

The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).

biological regulation

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

all

This term is the most general term possible

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

cell motility

Any process involved in the controlled movement of a cell that results in translocation of the cell from one place to another.

positive regulation of response to 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.

taxis

The directed movement of a motile cell or organism in response to an external stimulus.

chemotaxis

cell motion

Any process involved in the controlled movement of a cell.

cell chemotaxis

leukocyte migration

The movement of leukocytes within or between different tissues and organs of the body.

leukocyte chemotaxis

The movement of a leukocyte in response to an external stimulus.

inflammatory response

taxis

The directed movement of a motile cell or organism in response to an external stimulus.

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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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.

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.

extracellular space

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

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.

all

This term is the most general term possible

extracellular region part

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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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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:0006959	1.055e-04	0.0699	4 CCL2, CFH, CFHR1, IL6	30	humoral immune response
GO:0030595	1.028e-03	0.03961	3 CCL2, IL6, IL8	17	leukocyte chemotaxis
GO:0060326	1.028e-03	0.03961	3 CCL2, IL6, IL8	17	cell chemotaxis
GO:0002548	2.020e-03	0.00699	2 CCL2, IL6	3	monocyte chemotaxis
GO:0048584	2.085e-03	0.1608	4 CFH, CFHR1, IL6, IL8	69	positive regulation of response to stimulus
GO:0006952	2.351e-03	0.6128	6 CCL2, CFH, CFHR1, IL6, IL8, LGALS3BP	263	defense response
GO:0006954	2.435e-03	0.3565	5 CCL2, CFH, CFHR1, IL6, IL8	153	inflammatory response
GO:0050900	4.604e-03	0.0699	3 CCL2, IL6, IL8	30	leukocyte migration
GO:0002526	7.706e-03	0.08621	3 CFH, CFHR1, IL6	37	acute inflammatory response
GO:0007155	1.201e-02	0.8761	6	376	cell adhesion
GO:0022610	1.201e-02	0.8761	6	376	biological adhesion
GO:0009611	1.207e-02	0.5382	5 CCL2, CFH, CFHR1, IL6, IL8	231	response to wounding
GO:0048583	1.316e-02	0.2866	4 CFH, CFHR1, IL6, IL8	123	regulation of response to stimulus
GO:0040017	2.655e-02	0.03029	2 IL6, IL8	13	positive regulation of locomotion
GO:0048520	2.655e-02	0.03029	2 IL6, IL8	13	positive regulation of behavior
GO:0050920	2.655e-02	0.03029	2 IL6, IL8	13	regulation of chemotaxis
GO:0050921	2.655e-02	0.03029	2 IL6, IL8	13	positive regulation of chemotaxis
GO:0006955	2.842e-02	0.6874	5 CCL2, CFH, CFHR1, IL6, IL8	295	immune response
GO:0050795	2.958e-02	0.03262	2 IL6, IL8	14	regulation of behavior
GO:0006935	3.144e-02	0.1608	3 CCL2, IL6, IL8	69	chemotaxis
GO:0042330	3.144e-02	0.1608	3 CCL2, IL6, IL8	69	taxis
GO:0050776	3.633e-02	0.1724	3 CFH, CFHR1, IL6	74	regulation of immune response
GO:0002541	3.889e-02	0.03961	2 CFH, CFHR1	17	activation of plasma proteins during acute inflammatory response
GO:0006956	3.889e-02	0.03961	2 CFH, CFHR1	17	complement activation
GO:0045767	3.889e-02	0.03961	2 IL6, TNFAIP8	17	regulation of anti-apoptosis
GO:0002252	4.247e-02	0.1864	3 CFH, CFHR1, IL6	80	immune effector process
GO:0002684	4.411e-02	0.1911	3 CFH, CFHR1, IL6	82	positive regulation of immune system process
GO:0019079	4.828e-02	0.0466	2 CCL2, IL8	20	viral genome replication

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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:0005615	1.283e-03	0.6516	6 CCL2, CFH, CFHR1, IL6, IL8, LGALS3BP	246	extracellular space
GO:0005576	1.414e-03	1.854	9	700	extracellular region
GO:0044421	1.618e-03	1.025	7	387	extracellular region 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.

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

Id	Pvalue	ExpCount	Count	Size	Term
GO:0005125	3.397e-02	0.1511	3 CCL2, IL6, IL8	73	cytokine activity
GO:0008009	3.402e-02	0.03104	2 CCL2, IL8	15	chemokine activity
GO:0042379	3.402e-02	0.03104	2 CCL2, IL8	15	chemokine receptor 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.

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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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Id	Pvalue	ExpCount	Count	Size
Y	4.487e-04	0.06886	4 DDX3Y, EIF1AY, JARID1D, RPS4Y1	31

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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.

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 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 experiments that were part of the study, are separated by dashed vertical lines.

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Id	sample	Experiment	ExpName	Array	Syndrome	Cell.line
1Twin.CEL	1	2	DS-twin	hgu133plus2	Down	DS-twin 1
5CTwin.CEL	5	2	DS-twin	hgu133plus2	Down	DS-twin 5
2Twin.CEL	2	2	DS-twin	hgu133plus2	none	DS-twin 2
6Twin.CEL	6	2	DS-twin	hgu133plus2	none	DS-twin 6
E-GEOD-3407-raw-cel-1437949557.cel	1	4	Cockayne	hgu133a	CS	eGFP
E-GEOD-3860-raw-cel-1561690472.cel	17	5	HGPS	hgu133a	none	GM00038C
E-GEOD-3860-raw-cel-1561690223.cel	3	5	HGPS	hgu133a	none	GM00038C
E-GEOD-3860-raw-cel-1561690344.cel	10	5	HGPS	hgu133a	none	GM00038C
t21b 08-03.CEL	5	1	DS-CC	hgu133a	Down	DS-CC 5
t21d 08-03.CEL	7	1	DS-CC	hgu133a	Down	DS-CC 7
E-GEOD-3860-raw-cel-1561690215.cel	2	5	HGPS	hgu133a	HGPS	AG11513
ctrl c 08-03.CEL	3	1	DS-CC	hgu133a	none	DS-CC 3
E-GEOD-4219-raw-cel-1311956418.cel	13	7	Sph-mono	hgu133plus2	none	Sph-mon 1
46A.CEL	1	3	DS-mosaic	hgu133plus2	none	DS-mosaic 1
E-GEOD-3860-raw-cel-1561690352.cel	11	5	HGPS	hgu133a	HGPS	AG11498
E-GEOD-3860-raw-cel-1561690272.cel	7	5	HGPS	hgu133a	HGPS	AG11498
E-GEOD-3860-raw-cel-1561690480.cel	18	5	HGPS	hgu133a	HGPS	AG11498

Previous module | Next module Module #356, TG: 3.4, TC: 1.4, 21 probes, 21 Entrez genes, 17 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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