Module #275, TG: 3.6, TC: 1, 7 probes, 7 Entrez genes, 34 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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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.

nitrogen compound metabolic process

The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds; includes nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium.

nitric oxide biosynthetic process

The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.

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.

biosynthetic process

The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

regulation of biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.

positive regulation of biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.

positive regulation of metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an 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.

regulation of metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

regulation of cellular metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

positive regulation of cellular metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

regulation of cellular biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

positive regulation of cellular biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

cellular nitrogen compound metabolic process

The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.

cellular metabolic process

The chemical reactions and pathways by which individual cells transform chemical substances.

cellular biosynthetic process

The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

nitrogen compound biosynthetic process

The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.

regulation of nitric oxide biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

positive regulation of nitric oxide biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

nitric oxide metabolic process

The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.

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 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.

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 nitrogen compound metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.

positive regulation of nitrogen compound metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.

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

cellular metabolic process

The chemical reactions and pathways by which individual cells transform chemical substances.

positive regulation of metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

positive regulation of cellular process

regulation of metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

positive regulation of biological process

regulation of cellular process

regulation of biological process

positive regulation of biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.

positive regulation of nitrogen compound metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.

regulation of biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.

positive regulation of metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.

regulation of nitrogen compound metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.

regulation of cellular metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

positive regulation of cellular metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

cellular nitrogen compound metabolic process

The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.

cellular biosynthetic process

The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

positive regulation of cellular metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

regulation of cellular metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

positive regulation of cellular process

positive regulation of nitrogen compound metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.

positive regulation of biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.

regulation of cellular biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

positive regulation of cellular biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

nitrogen compound biosynthetic process

The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.

positive regulation of cellular biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

positive regulation of cellular metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.

regulation of cellular biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

nitric oxide biosynthetic process

The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.

regulation of nitric oxide biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

positive regulation of nitric oxide biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

positive regulation of nitric oxide biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

positive regulation of cellular biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

regulation of nitric oxide biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

positive regulation of nitric oxide biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

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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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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:0045429	3.628e-03	0.009046	2 INSR, SOD2	11	positive regulation of nitric oxide biosynthetic process
GO:0065008	3.687e-03	0.537	5 ABCA1, DHRS3, INSR, MXI1, SOD2	653	regulation of biological quality
GO:0051173	4.238e-03	0.009868	2 INSR, SOD2	12	positive regulation of nitrogen compound metabolic process
GO:0045428	4.846e-03	0.01069	2 INSR, SOD2	13	regulation of nitric oxide biosynthetic process
GO:0051171	6.884e-03	0.01316	2 INSR, SOD2	16	regulation of nitrogen compound metabolic process
GO:0006809	9.861e-03	0.01645	2 INSR, SOD2	20	nitric oxide biosynthetic process
GO:0046209	9.861e-03	0.01645	2 INSR, SOD2	20	nitric oxide metabolic process
GO:0048878	1.968e-02	0.1447	3 ABCA1, INSR, SOD2	176	chemical homeostasis
GO:0008285	2.321e-02	0.1562	3 CDKN1C, MXI1, SOD2	190	negative regulation of cell proliferation
GO:0001315	4.380e-02	0.0008224	1 SOD2	1	age-dependent response to reactive oxygen species
GO:0003068	4.380e-02	0.0008224	1 SOD2	1	regulation of systemic arterial blood pressure by acetylcholine
GO:0003069	4.380e-02	0.0008224	1 SOD2	1	vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure
GO:0003070	4.380e-02	0.0008224	1 SOD2	1	regulation of systemic arterial blood pressure by neurotransmitter
GO:0010260	4.380e-02	0.0008224	1 SOD2	1	organ senescence
GO:0019087	4.380e-02	0.0008224	1 INSR	1	transformation of host cell by virus
GO:0019430	4.380e-02	0.0008224	1 SOD2	1	removal of superoxide radicals
GO:0030801	4.380e-02	0.0008224	1 ABCA1	1	positive regulation of cyclic nucleotide metabolic process
GO:0030804	4.380e-02	0.0008224	1 ABCA1	1	positive regulation of cyclic nucleotide biosynthetic process
GO:0030810	4.380e-02	0.0008224	1 ABCA1	1	positive regulation of nucleotide biosynthetic process
GO:0030816	4.380e-02	0.0008224	1 ABCA1	1	positive regulation of cAMP metabolic process
GO:0030819	4.380e-02	0.0008224	1 ABCA1	1	positive regulation of cAMP biosynthetic process
GO:0044003	4.380e-02	0.0008224	1 INSR	1	modification by symbiont of host morphology or physiology
GO:0045981	4.380e-02	0.0008224	1 ABCA1	1	positive regulation of nucleotide metabolic process
GO:0048773	4.380e-02	0.0008224	1 SOD2	1	erythrophore differentiation
GO:0051817	4.380e-02	0.0008224	1 INSR	1	modification of morphology or physiology of other organism during symbiotic interaction
GO:0055093	4.380e-02	0.0008224	1 SOD2	1	response to hyperoxia
GO:0060267	4.380e-02	0.0008224	1 INSR	1	positive regulation of respiratory burst
GO:0044271	4.895e-02	0.04934	2 INSR, SOD2	60	nitrogen compound biosynthetic process

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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:0045121	1.724e-02	0.03885	2 ABCA1, INSR	44	membrane raft
GO:0005899	2.318e-02	0.0008829	1 INSR	1	insulin receptor complex

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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.

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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
E-GEOD-4219-raw-cel-1311956614.cel	18	7	Sph-mono	hgu133plus2	none	Sph-mon 1
F055_WBS.CEL	14	8	WBS	hgu133plus2	WBS	WBS 1
E-GEOD-4219-raw-cel-1311956321.cel	9	7	Sph-mono	hgu133plus2	none	Sph-mon 1
1Twin.CEL	1	2	DS-twin	hgu133plus2	Down	DS-twin 1
E-TABM-263-raw-cel-1515486371.cel	37	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486031.cel	20	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486131.cel	25	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485811.cel	9	6	Cycle	hgu133a2	none	Cycle 1
2Twin.CEL	2	2	DS-twin	hgu133plus2	none	DS-twin 2
E-TABM-263-raw-cel-1515485891.cel	13	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485871.cel	12	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956138.cel	4	7	Sph-mono	hgu133plus2	none	Sph-mon 1
5CTwin.CEL	5	2	DS-twin	hgu133plus2	Down	DS-twin 5
E-GEOD-3407-raw-cel-1437949854.cel	7	4	Cockayne	hgu133a	CS	eGFP
E-TABM-263-raw-cel-1515486171.cel	27	6	Cycle	hgu133a2	none	Cycle 1
ctrl a 08-03.CEL	1	1	DS-CC	hgu133a	none	DS-CC 1
ctrl c 08-03.CEL	3	1	DS-CC	hgu133a	none	DS-CC 3
E-GEOD-4219-raw-cel-1311956398.cel	12	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486231.cel	30	6	Cycle	hgu133a2	none	Cycle 1
ctrl b 08-03.CEL	2	1	DS-CC	hgu133a	none	DS-CC 2
1104_CNTL.CEL	3	8	WBS	hgu133plus2	none	WBS 1
E-TABM-263-raw-cel-1515486271.cel	32	6	Cycle	hgu133a2	none	Cycle 1
3Twin.CEL	3	2	DS-twin	hgu133plus2	Down	DS-twin 3
t21c 08-03.CEL	6	1	DS-CC	hgu133a	Down	DS-CC 6
E-GEOD-4219-raw-cel-1311956275.cel	8	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486331.cel	35	6	Cycle	hgu133a2	none	Cycle 1
4Twin.CEL	4	2	DS-twin	hgu133plus2	none	DS-twin 4
8495_CNTL.CEL	10	8	WBS	hgu133plus2	none	WBS 1
9118_CNTL.CEL	11	8	WBS	hgu133plus2	none	WBS 1
E-GEOD-3860-raw-cel-1561690376.cel	13	5	HGPS	hgu133a	HGPS	AG11513
E-GEOD-4219-raw-cel-1311956418.cel	13	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486291.cel	33	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956634.cel	19	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-GEOD-4219-raw-cel-1311956083.cel	2	7	Sph-mono	hgu133plus2	none	Sph-mon 1

Previous module | Next module Module #275, TG: 3.6, TC: 1, 7 probes, 7 Entrez genes, 34 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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