Module #59, TG: 4, TC: 1.4, 30 probes, 30 Entrez genes, 13 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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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).

anatomical structure morphogenesis

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

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.

regulation of response to external stimulus

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

positive regulation of response to external stimulus

Any process that activates, maintains or increases the rate of a response to an external stimulus.

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.

locomotion

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

regulation of locomotion

Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.

positive regulation of locomotion

Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.

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.

positive regulation of behavior

Any process that activates or increases the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.

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.

anatomical structure formation

The process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. 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.

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.

regulation of behavior

Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.

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 chemotaxis

Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

positive regulation of chemotaxis

Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

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 locomotion

Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.

regulation of locomotion

Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.

positive regulation of biological process

regulation of response to stimulus

positive regulation of response to stimulus

regulation of biological process

anatomical structure formation

anatomical structure morphogenesis

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

positive regulation of locomotion

Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.

positive regulation of response to stimulus

positive regulation of behavior

Any process that activates or increases the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.

regulation of behavior

Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.

regulation of response to external stimulus

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

positive regulation of response to external stimulus

Any process that activates, maintains or increases the rate of a response to an external stimulus.

taxis

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

chemotaxis

positive regulation of chemotaxis

Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

regulation of chemotaxis

Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

positive regulation of chemotaxis

Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

positive regulation of chemotaxis

Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

positive regulation of chemotaxis

Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

positive regulation of response to external stimulus

Any process that activates, maintains or increases the rate of a response to an external stimulus.

regulation of chemotaxis

Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

positive regulation of behavior

Any process that activates or increases the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli.

regulation of chemotaxis

Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.

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:0040017	3.419e-03	0.03941	3 IL6, IL8, VEGFA	12	positive regulation of locomotion
GO:0048520	3.419e-03	0.03941	3 IL6, IL8, VEGFA	12	positive regulation of behavior
GO:0050795	3.419e-03	0.03941	3 IL6, IL8, VEGFA	12	regulation of behavior
GO:0050920	3.419e-03	0.03941	3 IL6, IL8, VEGFA	12	regulation of chemotaxis
GO:0050921	3.419e-03	0.03941	3 IL6, IL8, VEGFA	12	positive regulation of chemotaxis
GO:0048646	7.828e-03	0.3514	5 ANGPTL4, IL6, IL8, NR4A3, VEGFA	107	anatomical structure formation
GO:0050930	1.132e-02	0.009851	2 IL8, VEGFA	3	induction of positive chemotaxis
GO:0032103	1.196e-02	0.06568	3 IL6, IL8, VEGFA	20	positive regulation of response to external stimulus
GO:0050900	1.288e-02	0.06896	3 IL6, IL8, VEGFA	21	leukocyte migration
GO:0001525	2.203e-02	0.2463	4 ANGPTL4, IL6, IL8, VEGFA	75	angiogenesis
GO:0050918	2.457e-02	0.01642	2 IL8, VEGFA	5	positive chemotaxis
GO:0050926	2.457e-02	0.01642	2 IL8, VEGFA	5	regulation of positive chemotaxis
GO:0050927	2.457e-02	0.01642	2 IL8, VEGFA	5	positive regulation of positive chemotaxis
GO:0009605	2.579e-02	0.8275	6 IL6, IL8, JMJD3, NR4A3, THBD, VEGFA	252	response to external stimulus
GO:0048514	3.764e-02	0.3021	4 ANGPTL4, IL6, IL8, VEGFA	92	blood vessel morphogenesis
GO:0002687	4.017e-02	0.02299	2 IL6, VEGFA	7	positive regulation of leukocyte migration
GO:0032101	4.050e-02	0.1215	3 IL6, IL8, VEGFA	37	regulation of response to external stimulus
GO:0002685	4.847e-02	0.02627	2 IL6, VEGFA	8	regulation of leukocyte migration

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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	5.193e-05	1.282	10	445	extracellular region
GO:0044421	6.294e-05	0.6828	8	237	extracellular region part
GO:0005615	4.793e-04	0.3976	6 ANGPTL4, DKK2, IL6, IL8, THBD, VEGFA	138	extracellular space
GO:0005578	2.366e-02	0.3111	4 ANGPTL4, DPT, MFAP4, VEGFA	108	proteinaceous extracellular matrix
GO:0031012	2.650e-02	0.3284	4 ANGPTL4, DPT, MFAP4, VEGFA	114	extracellular matrix

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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	4.042e-02	0.09979	3 IL6, IL8, VEGFA	34	cytokine activity
GO:0005102	4.193e-02	0.8687	6 ANGPTL4, IL6, IL8, MFAP4, PDGFD, VEGFA	296	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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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 a 08-03.CEL	1	1	DS-CC	hgu133a	none	DS-CC 1
ctrl b 08-03.CEL	2	1	DS-CC	hgu133a	none	DS-CC 2
E-TABM-263-raw-cel-1515486231.cel	30	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486331.cel	35	6	Cycle	hgu133a2	none	Cycle 1
ctrl c 08-03.CEL	3	1	DS-CC	hgu133a	none	DS-CC 3
E-TABM-263-raw-cel-1515485851.cel	11	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956418.cel	13	7	Sph-mono	hgu133plus2	none	Sph-mon 1
2Twin.CEL	2	2	DS-twin	hgu133plus2	none	DS-twin 2
t21c 08-03.CEL	6	1	DS-CC	hgu133a	Down	DS-CC 6
t21b 08-03.CEL	5	1	DS-CC	hgu133a	Down	DS-CC 5
5CTwin.CEL	5	2	DS-twin	hgu133plus2	Down	DS-twin 5
6Twin.CEL	6	2	DS-twin	hgu133plus2	none	DS-twin 6
1Twin.CEL	1	2	DS-twin	hgu133plus2	Down	DS-twin 1

Previous module | Next module Module #59, TG: 4, TC: 1.4, 30 probes, 30 Entrez genes, 13 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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