Module #336, TG: 3.4, TC: 1.8, 40 probes, 40 Entrez genes, 3 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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generation of a signal involved in cell-cell signaling

The cellular process by which a physical entity or change in state, a signal, is created that originates in one cell and is used to transfer information to another cell. This process begins with the initial formation of the signal and ends with the mature form and placement of the signal.

secretion

The controlled release of a substance by a cell, a group of cells, or a tissue.

transport

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism.

cell communication

Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

cell-cell signaling

Any process that mediates the transfer of information from one cell to another.

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.

hormone transport

The directed movement of hormones into, out of, within or between cells.

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.

regulation of cell communication

Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

regulation of hormone levels

Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action.

positive regulation of follicle-stimulating hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

negative regulation of follicle-stimulating hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

positive regulation of hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

gonadotropin secretion

The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone.

regulation of gonadotropin secretion

Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin.

negative regulation of gonadotropin secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a gonadotropin.

positive regulation of gonadotropin secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin.

regulation of localization

Any process that modulates the frequency, rate or extent of any process by which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.

hormone secretion

The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.

regulation of follicle-stimulating hormone secretion

Any process that modulates the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

regulation of hormone secretion

Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

follicle-stimulating hormone secretion

The regulated release of follicle-stimulating hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary.

negative regulation of hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

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.

positive regulation of cellular process

Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

negative regulation of cellular process

Any process that stops, prevents or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

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.

regulation of cellular process

Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

regulation of secretion

Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

positive regulation of secretion

Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

negative regulation of secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

regulation of transport

Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

positive regulation of transport

Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

negative regulation of transport

Any process that stops, prevents or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

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.

establishment of localization

The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.

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.

all

This term is the most general term possible

positive regulation of cellular process

negative regulation of cellular process

positive regulation of biological process

negative regulation of biological process

regulation of cellular process

regulation of localization

Any process that modulates the frequency, rate or extent of any process by which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.

establishment of localization

The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.

regulation of biological process

regulation of cell communication

positive regulation of cellular process

negative regulation of cellular process

regulation of transport

Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

positive regulation of transport

Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

negative regulation of transport

Any process that stops, prevents or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

positive regulation of hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

negative regulation of hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

generation of a signal involved in cell-cell signaling

regulation of hormone secretion

Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

positive regulation of hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

negative regulation of hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

positive regulation of transport

Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

negative regulation of transport

Any process that stops, prevents or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

hormone secretion

The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.

regulation of secretion

Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

positive regulation of secretion

Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

negative regulation of secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

hormone secretion

The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.

hormone transport

The directed movement of hormones into, out of, within or between cells.

negative regulation of gonadotropin secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a gonadotropin.

positive regulation of gonadotropin secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin.

positive regulation of hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

regulation of gonadotropin secretion

Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin.

negative regulation of hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

regulation of hormone secretion

Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell or group of cells.

positive regulation of secretion

Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

negative regulation of secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of a substance from a cell or group of cells.

negative regulation of gonadotropin secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a gonadotropin.

positive regulation of gonadotropin secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin.

positive regulation of follicle-stimulating hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

negative regulation of follicle-stimulating hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

regulation of follicle-stimulating hormone secretion

Any process that modulates the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

positive regulation of follicle-stimulating hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

negative regulation of follicle-stimulating hormone secretion

Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of follicle-stimulating hormone.

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.

proteinaceous extracellular matrix

A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity.

extracellular matrix

A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as in plants).

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:0032276	7.275e-03	0.01459	2 INHBA, INHBB	3	regulation of gonadotropin secretion
GO:0032277	7.275e-03	0.01459	2 INHBA, INHBB	3	negative regulation of gonadotropin secretion
GO:0032278	7.275e-03	0.01459	2 INHBA, INHBB	3	positive regulation of gonadotropin secretion
GO:0046880	7.275e-03	0.01459	2 INHBA, INHBB	3	regulation of follicle-stimulating hormone secretion
GO:0046881	7.275e-03	0.01459	2 INHBA, INHBB	3	positive regulation of follicle-stimulating hormone secretion
GO:0046882	7.275e-03	0.01459	2 INHBA, INHBB	3	negative regulation of follicle-stimulating hormone secretion
GO:0032274	1.238e-02	0.01946	2 INHBA, INHBB	4	gonadotropin secretion
GO:0046884	1.238e-02	0.01946	2 INHBA, INHBB	4	follicle-stimulating hormone secretion
GO:0007267	1.559e-02	1.24	7	255	cell-cell signaling
GO:0048856	1.923e-02	5.871	15	1207	anatomical structure development
GO:0010817	2.165e-02	0.3259	4 CYP26B1, INHBA, INHBB, PBX1	67	regulation of hormone levels
GO:0032502	2.384e-02	9.095	19	1870	developmental process
GO:0042036	3.099e-02	0.03405	2 INHBA, INHBB	7	negative regulation of cytokine biosynthetic process
GO:0007399	3.410e-02	1.955	8	402	nervous system development
GO:0031128	3.755e-02	0.03891	2 HOXA11, SALL1	8	induction
GO:0045168	3.755e-02	0.03891	2 HOXA11, SALL1	8	cell-cell signaling involved in cell fate commitment
GO:0030326	4.115e-02	0.18	3 CYP26B1, HOXA11, MSX1	37	embryonic limb morphogenesis
GO:0035113	4.115e-02	0.18	3 CYP26B1, HOXA11, MSX1	37	embryonic appendage morphogenesis
GO:0046887	4.419e-02	0.04377	2 INHBA, INHBB	9	positive regulation of hormone secretion
GO:0046888	4.419e-02	0.04377	2 INHBA, INHBB	9	negative regulation of hormone secretion

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.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0005576	3.482e-04	3.187	13	673	extracellular region
GO:0005578	2.862e-03	0.7245	6 ADAMTS5, COL8A2, COMP, DPT, LTBP1, MMP3	153	proteinaceous extracellular matrix
GO:0031012	3.876e-03	0.7718	6 ADAMTS5, COL8A2, COMP, DPT, LTBP1, MMP3	163	extracellular matrix
GO:0044421	9.778e-03	1.78	8	376	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:0005179	2.432e-02	0.1239	3 CGB, INHBA, INHBB	27	hormone activity
GO:0005102	3.270e-02	1.836	8	400	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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Id	Pvalue	ExpCount	Count	Size	Term
04350	8.116e-03	0.2619	4 COMP, INHBA, INHBB, LTBP1	64	TGF-beta signaling pathway

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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.

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
ctrl c 08-03.CEL	3	1	DS-CC	hgu133a	none	DS-CC 3
E-GEOD-3860-raw-cel-1561690416.cel	15	5	HGPS	hgu133a	none	GM0316B
E-GEOD-3860-raw-cel-1561690360.cel	12	5	HGPS	hgu133a	none	GM0316B

Previous module | Next module Module #336, TG: 3.4, TC: 1.8, 40 probes, 40 Entrez genes, 3 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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