Module #514, TG: 3.2, TC: 1.2, 18 probes, 18 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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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.

oxidation reduction

The process of removal or addition of one or more electrons with or without the concomitant removal or addition of a proton or protons.

lipid metabolic process

The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

digestion

The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.

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.

steroid metabolic process

The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

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.

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.

multicellular organismal process

Any biological process, occurring at the level of a multicellular organism, pertinent to its function.

cellular metabolic process

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

primary metabolic process

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

cellular biosynthetic process

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

cellular lipid metabolic process

The chemical reactions and pathways involving lipids, as carried out by individual cells.

all

This term is the most general term possible

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.

steroid metabolic process

The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

cellular lipid metabolic process

The chemical reactions and pathways involving lipids, as carried out by individual cells.

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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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molecular_function

Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.

catalytic activity

Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

aldo-keto reductase activity

Catalysis of the NADPH-dependent reduction of carbonyl compounds.

binding

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

oxidoreductase activity

Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

steroid dehydrogenase activity

Catalysis of an oxidation-reduction (redox) reaction in which one substrate is a sterol derivative.

oxidoreductase activity, acting on CH-OH group of donors

Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

oxidoreductase activity, acting on the CH-CH group of donors

Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor

Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.

carboxylic acid binding

Interacting selectively with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).

bile acid binding

Interacting selectively with bile acids, any of a group of steroid carboxylic acids occurring in bile.

steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP, and in which one substrate is a sterol derivative.

3-alpha-hydroxysteroid dehydrogenase (A-specific) activity

Catalysis of the reaction: NAD(P)+ + androsterone = NAD(P)H + H+ + 5-alpha-androstane-3,17-dione. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD(P)+.

trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity

Catalysis of the reaction: NADP+ + trans-1,2-dihydrobenzene-1,2-diol = NADPH + catechol.

testosterone 17-beta-dehydrogenase activity

Catalysis of the reaction: testosterone + NAD+ = androst-4-ene-3,17-dione + NADH.

all

This term is the most general term possible

steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP, and in which one substrate is a sterol derivative.

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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:0007586	2.491e-03	0.0542	3 AKR1B10, AKR1C1, AKR1C2	26	digestion
GO:0055114	6.189e-03	0.7629	6	366	oxidation reduction
GO:0008202	6.890e-03	0.2314	4 AKR1B10, AKR1C1, AKR1C2, HSD17B6	111	steroid metabolic process
GO:0006692	1.290e-02	0.01876	2 AKR1C2, AKR1C3	9	prostanoid metabolic process
GO:0006693	1.290e-02	0.01876	2 AKR1C2, AKR1C3	9	prostaglandin metabolic process
GO:0032787	1.630e-02	0.3085	4 AKR1C1, AKR1C2, AKR1C3, KYNU	148	monocarboxylic acid metabolic process
GO:0032501	2.233e-02	3.358	10	1611	multicellular organismal process
GO:0006805	2.287e-02	0.0271	2 AKR1C1, KYNU	13	xenobiotic metabolic process
GO:0009410	3.110e-02	0.03335	2 AKR1C1, KYNU	16	response to xenobiotic stimulus
GO:0006690	3.383e-02	0.03544	2 AKR1C2, AKR1C3	17	icosanoid metabolic process
GO:0044255	3.510e-02	0.7421	5	356	cellular lipid metabolic 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.

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

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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:0047115	1.042e-05	0.007081	3 AKR1C1, AKR1C2, AKR1C3	3	trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity
GO:0033764	1.320e-05	0.03068	4 AKR1C1, AKR1C2, AKR1C3, HSD17B6	13	steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016229	2.038e-05	0.03541	4 AKR1C1, AKR1C2, AKR1C3, HSD17B6	15	steroid dehydrogenase activity
GO:0016616	1.545e-04	0.1581	5	67	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016614	1.920e-04	0.1676	5	71	oxidoreductase activity, acting on CH-OH group of donors
GO:0004033	5.577e-04	0.02596	3 AKR1B10, AKR1C1, AKR1C3	11	aldo-keto reductase activity
GO:0047026	1.288e-03	0.004721	2 AKR1C2, AKR1C3	2	3-alpha-hydroxysteroid dehydrogenase (A-specific) activity
GO:0016628	1.429e-03	0.03777	3 AKR1C1, AKR1C2, AKR1C3	16	oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
GO:0032052	3.028e-03	0.007081	2 AKR1C1, AKR1C2	3	bile acid binding
GO:0050327	3.028e-03	0.007081	2 AKR1C3, HSD17B6	3	testosterone 17-beta-dehydrogenase activity
GO:0031406	1.383e-02	0.01652	2 AKR1C1, AKR1C2	7	carboxylic acid binding
GO:0016627	1.401e-02	0.09677	3 AKR1C1, AKR1C2, AKR1C3	41	oxidoreductase activity, acting on the CH-CH group of donors
GO:0016491	2.257e-02	0.9441	6	400	oxidoreductase activity

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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
00980	1.528e-02	0.1239	3 AKR1C1, AKR1C2, AKR1C3	37	Metabolism of xenobiotics by cytochrome P450

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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-1311956457.cel	14	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486311.cel	34	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956138.cel	4	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486211.cel	29	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485791.cel	8	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956614.cel	18	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-GEOD-4219-raw-cel-1311956321.cel	9	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-GEOD-3860-raw-cel-1561690392.cel	14	5	HGPS	hgu133a	none	GMO8398C
E-TABM-263-raw-cel-1515485651.cel	1	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485671.cel	2	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485771.cel	7	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485811.cel	9	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485891.cel	13	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956824.cel	24	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-GEOD-4219-raw-cel-1311956358.cel	10	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486371.cel	37	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956178.cel	6	7	Sph-mono	hgu133plus2	none	Sph-mon 1

Previous module | Next module Module #514, TG: 3.2, TC: 1.2, 18 probes, 18 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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