Module #107, TG: 2.4, TC: 2.2, 189 probes, 185 Entrez genes, 4 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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reproduction

The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.

aggressive behavior

A behavioral interaction between organisms in which one organism has the intention of inflicting physical damage on another individual.

maternal aggressive behavior

Aggressive behavior of a female to protect her offspring from a threat.

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.

mating behavior

The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.

mating

The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.

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.

reproductive behavior

The specific actions or reactions of an organism that are associated with reproduction.

reproductive process

A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

multicellular organismal process

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

multicellular organism reproduction

The biological process by which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

reproductive behavior in a multicellular organism

The specific actions or reactions of an organism that are associated with reproduction in a multicellular organism.

regulation of female receptivity

Any process that modulates the frequency, rate or extent of the willingness or readiness of a female to receive male advances.

reproductive process in a multicellular organism

The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.

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.

multi-organism process

Any process by which an organism has an effect on another organism of the same or different species.

behavioral interaction between organisms

Any process by which an organism has a behavioral effect on another organism of the same or different species.

female mating behavior

The specific actions or reactions of a female organism that are associated with reproduction.

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.

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reproductive process

multicellular organism reproduction

The biological process by which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

reproductive process in a multicellular organism

The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.

mating

The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.

reproductive process in a multicellular organism

The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.

mating behavior

The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.

reproductive behavior in a multicellular organism

The specific actions or reactions of an organism that are associated with reproduction in a multicellular organism.

reproductive behavior

The specific actions or reactions of an organism that are associated with reproduction.

behavioral interaction between organisms

Any process by which an organism has a behavioral effect on another organism of the same or different species.

mating behavior

The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.

female mating behavior

The specific actions or reactions of a female organism that are associated with reproduction.

regulation of female receptivity

Any process that modulates the frequency, rate or extent of the willingness or readiness of a female to receive male advances.

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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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intracellular

The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

photoreceptor outer segment

The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.

membrane

Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.

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.

cell

The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

cilium

A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.

nonmotile primary cilium

An immotile primary cilium that may be missing the central pair of microtubules, or the central pair of microtubules and outer dynein arms. Some primary cilia also have altered arrangements of outer microtubules (fewer than nine and/or not always present as doublets). Nonmotile primary cilia typically function as sensory organelles that concentrate and organize sensory signaling molecules.

photoreceptor outer segment membrane

The membrane surrounding the outer segment of a vertebrate photoreceptor.

cell projection

A prolongation or process extending from a cell, e.g. a flagellum or axon.

organelle

Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.

intracellular organelle

Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

organelle part

Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane.

intracellular part

Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

cilium part

Any constituent part of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.

intracellular organelle part

A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.

cell projection part

Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon.

cell part

Any constituent part of a cell, the basic structural and functional unit of all organisms.

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cell part

Any constituent part of a cell, the basic structural and functional unit of all organisms.

organelle part

intracellular organelle part

intracellular part

cell projection part

Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon.

intracellular organelle

intracellular organelle part

cilium part

photoreceptor outer segment membrane

The membrane surrounding the outer segment of a vertebrate photoreceptor.

cilium part

photoreceptor outer segment membrane

The membrane surrounding the outer segment of a vertebrate photoreceptor.

HELP

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.

N-acetylgalactosamine-4-sulfatase activity

Catalysis of the hydrolysis of the 4-sulfate groups of the N-acetyl-D-galactosamine 4-sulfate units of chondroitin sulfate and dermatan sulfate.

transporter activity

Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

transmembrane transporter activity

Enables the transfer of a substance from one side of a membrane to the other.

sulfuric ester hydrolase activity

Catalysis of the reaction: RSO-R' + H2O = RSOOH + R'H. This reaction is the hydrolysis of any sulfuric ester bond, any ester formed from sulfuric acid, O=SO(OH)2.

vitamin transporter activity

Enables the directed movement of vitamins into, out of, within or between cells. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.

hydrolase activity

Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

hydrolase activity, acting on ester bonds

Catalysis of the hydrolysis of any ester bond.

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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:0009605	6.718e-03	7.48	19	536	response to external stimulus
GO:0002125	7.880e-03	0.02791	2 AVPR1A, OXT	2	maternal aggressive behavior
GO:0045924	7.880e-03	0.02791	2 AVPR1A, OXT	2	regulation of female receptivity
GO:0060180	7.880e-03	0.02791	2 AVPR1A, OXT	2	female mating behavior
GO:0051180	1.144e-02	0.3349	4 GPR172B, SLC22A4, SLC23A1, SLC46A1	24	vitamin transport
GO:0046006	1.407e-02	0.1535	3 FOXP3, IL12B, IL2	11	regulation of activated T cell proliferation
GO:0002118	1.861e-02	0.04186	2 AVPR1A, OXT	3	aggressive behavior
GO:0009584	2.898e-02	0.2093	3 ABCA4, GNAT1, GNAT2	15	detection of visible light
GO:0050798	2.898e-02	0.2093	3 FOXP3, IL12B, IL2	15	activated T cell proliferation
GO:0003079	3.034e-02	0.05582	2 AVPR1A, OXT	4	positive regulation of natriuresis
GO:0051345	3.105e-02	2.093	8	150	positive regulation of hydrolase activity
GO:2000021	3.239e-02	0.8094	5 ALOX12, AVPR1A, GCLM, OXT, XCR1	58	regulation of ion homeostasis
GO:0006935	3.296e-02	2.121	8	152	chemotaxis
GO:0042330	3.296e-02	2.121	8	152	taxis
GO:0006488	4.369e-02	0.06977	2 ALG2, SRD5A3	5	dolichol-linked oligosaccharide biosynthetic process
GO:0042713	4.369e-02	0.06977	2 AVPR1A, OXT	5	sperm ejaculation

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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.

Id	Pvalue	ExpCount	Count	Size	Term
GO:0042622	8.544e-03	0.04224	2 GNAT1, GNAT2	3	photoreceptor outer segment membrane
GO:0005576	1.358e-02	19.81	34	1407	extracellular region
GO:0045177	3.085e-02	2.394	8	170	apical part of cell

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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:0051183	3.419e-03	0.2485	4 GPR172B, SLC22A4, SLC23A1, SLC46A1	17	vitamin transporter activity
GO:0003943	6.866e-03	0.02924	2 ARSB, GALNS	2	N-acetylgalactosamine-4-sulfatase activity
GO:0001653	2.763e-02	1.199	6 AVPR1A, CXCR2, CXCR3, F2RL2, FPR3, XCR1	82	peptide receptor activity
GO:0008528	2.763e-02	1.199	6 AVPR1A, CXCR2, CXCR3, F2RL2, FPR3, XCR1	82	peptide receptor activity, G-protein coupled
GO:0042277	3.523e-02	2.222	8	152	peptide binding
GO:0001637	4.131e-02	0.2632	3 CXCR2, CXCR3, XCR1	18	G-protein chemoattractant receptor activity
GO:0004950	4.131e-02	0.2632	3 CXCR2, CXCR3, XCR1	18	chemokine receptor activity
GO:0015291	4.525e-02	2.339	8	160	secondary active transmembrane transporter activity
GO:0016627	4.582e-02	0.5702	4 ACOX1, DPYD, IVD, SRD5A3	39	oxidoreductase activity, acting on the CH-CH group of donors

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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.

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

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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.

Text color indicates correlation and anti-correlation: genes of the same color are correlated, both move up or down in the module samples (listed below). Genes of different color are anti-correlated, they have opposite behavior in the module samples.

Note, that text color of the individual genes should be interpreted together with the coloring of the samples below. For red samples, red genes have a higher expression (compared to the average gene expression level), green genes have a lower expression.

Green samples have opposite behavior, in these red genes have a lower expression, green genes have a higher expression.

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 height of each bar corresponds to the weighted mean expression of the module genes. The weights are the gene scores of the module and they are positive for the genes listed in red above and they are negative for the genes that are listed in green.

Bars going up correspond to samples listed in red (the ones that are different enough to included in the module). In these samples the red module genes are highly expressed, and the green module genes are lowly expressed. The behavior of the genes is the opposite for bars going down.

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 species and tissues that were part of the study, are separated by dashed vertical lines.

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Id	species	tissue	sex	individual
mml_kd_f_ca1	mml	kd	f	_
mml_kd_m_ca1	mml	kd	m	_
mml_lv_f_ca1	mml	lv	f	_
mml_lv_m_ca1	mml	lv	m	_

Previous module | Next module Module #107, TG: 2.4, TC: 2.2, 189 probes, 185 Entrez genes, 4 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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