Module #295, TG: 2.4, TC: 2.4, 101 probes, 101 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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system process

A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.

secretion

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

transport

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism by means of some external agent such as a transporter or pore.

ion transport

The directed movement of charged atoms or small charged molecules into, out of, within or between cells by means of some external agent such as a transporter or pore.

excretion

The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.

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.

multicellular organismal process

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

localization

Any process by which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location.

establishment of localization

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

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establishment of localization

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

excretion

The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.

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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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plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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.

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.

vacuole

A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

integral to membrane

Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane.

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.

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

brush border

Dense covering of microvilli on the apical surface of epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.

apical plasma membrane

The region of the plasma membrane located at the apical end of the cell.

intrinsic to membrane

Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane.

cell projection membrane

The portion of the plasma membrane surrounding a cell surface projection.

brush border membrane

The portion of the plasma membrane surrounding the brush border.

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.

membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. 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.

intracellular membrane-bounded organelle

Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. 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.

membrane part

Any constituent part of a membrane, a 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.

cytoplasmic part

Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

plasma membrane part

Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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.

apical part of cell

The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.

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cell part

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

intracellular membrane-bounded organelle

intracellular part

membrane 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

plasma membrane part

Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

cytoplasmic part

Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

vacuole

apical plasma membrane

The region of the plasma membrane located at the apical end of the cell.

cell projection membrane

The portion of the plasma membrane surrounding a cell surface projection.

brush border membrane

The portion of the plasma membrane surrounding the brush border.

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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.

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.

secondary active transmembrane transporter activity

Catalysis of the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Chemiosmotic sources of energy include uniport, symport or antiport.

cation transmembrane transporter activity

Catalysis of the transfer of cation from one side of the membrane to the other.

ion transmembrane transporter activity

Catalysis of the transfer of an ion from one side of a membrane to the other.

symporter activity

Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.

active transmembrane transporter activity

Catalysis of the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction.

inorganic cation transmembrane transporter activity

Catalysis of the transfer of inorganic cations from one side of a membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage.

substrate-specific transmembrane transporter activity

Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other.

substrate-specific transporter activity

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

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substrate-specific transmembrane transporter activity

Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other.

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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:0007588	4.984e-05	0.4619	7	24	excretion
GO:0006811	1.383e-03	6.389	19	332	ion transport
GO:0006814	1.557e-02	0.9045	6	47	sodium ion transport
GO:0032836	2.127e-02	0.03849	2 COL4A3, COL4A4	2	glomerular basement membrane development
GO:0015696	4.679e-02	0.05773	2 RHAG, RHCG	3	ammonium transport
GO:0035313	4.679e-02	0.05773	2 SCNN1B, SCNN1G	3	wound healing, spreading of epidermal cells
GO:0044319	4.679e-02	0.05773	2 SCNN1B, SCNN1G	3	wound healing, spreading of cells

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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:0045177	1.194e-06	1.434	12	75	apical part of cell
GO:0016324	8.950e-06	1.128	10	59	apical plasma membrane
GO:0044459	5.815e-04	13.79	30	721	plasma membrane part
GO:0031526	2.313e-03	0.2486	4 ATP6V0A4, CUBN, SLC34A1, TRPM6	13	brush border membrane
GO:0031224	4.519e-03	30.93	48	1617	intrinsic to membrane
GO:0016021	5.579e-03	30.29	47	1584	integral to membrane
GO:0005903	7.217e-03	0.3443	4 ATP6V0A4, CUBN, SLC34A1, TRPM6	18	brush border
GO:0005773	7.543e-03	1.76	8	92	vacuole
GO:0000323	1.140e-02	1.454	7	76	lytic vacuole
GO:0005764	1.140e-02	1.454	7	76	lysosome
GO:0005886	1.173e-02	21.67	36	1133	plasma membrane
GO:0044425	1.343e-02	36.32	52	1899	membrane part
GO:0034706	1.919e-02	0.05738	2 SCNN1B, SCNN1G	3	sodium channel complex
GO:0031253	2.156e-02	0.8224	5 ATP6V0A4, CUBN, FERMT1, SLC34A1, TRPM6	43	cell projection membrane
GO:0005587	3.282e-02	0.0765	2 COL4A3, COL4A4	4	collagen type IV
GO:0030935	4.785e-02	0.09563	2 COL4A3, COL4A4	5	sheet-forming collagen

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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:0005215	1.508e-04	8.751	25	454	transporter activity
GO:0022857	1.911e-04	7.093	22	368	transmembrane transporter activity
GO:0022892	3.845e-04	7.479	22	388	substrate-specific transporter activity
GO:0022891	6.432e-04	6.592	20	342	substrate-specific transmembrane transporter activity
GO:0015075	3.500e-03	5.783	17	300	ion transmembrane transporter activity
GO:0015293	5.783e-03	1.079	7	56	symporter activity
GO:0022890	6.563e-03	1.484	8	77	inorganic cation transmembrane transporter activity
GO:0022804	9.947e-03	2.506	10	130	active transmembrane transporter activity
GO:0015291	1.047e-02	1.619	8	84	secondary active transmembrane transporter activity
GO:0008519	1.757e-02	0.03855	2 RHAG, RHCG	2	ammonium transmembrane transporter activity
GO:0015095	1.757e-02	0.03855	2 CLDN16, ZDHHC13	2	magnesium ion transmembrane transporter activity
GO:0008028	2.338e-02	0.1735	3 SLC10A2, SLC16A2, SLC16A4	9	monocarboxylic acid transmembrane transporter activity
GO:0046873	2.708e-02	1.079	6	56	metal ion transmembrane transporter activity
GO:0030506	3.931e-02	0.05783	2 RHAG, RHCG	3	ankyrin binding
GO:0051739	3.931e-02	0.05783	2 RHAG, RHCG	3	ammonia transmembrane transporter activity
GO:0016811	4.188e-02	0.4819	4 ACER3, ASAH1, ASPA, FAAH	25	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0008324	4.255e-02	4.376	12	227	cation transmembrane transporter 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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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.

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
oan_kd_m_ca1	oan	kd	m	_
mdo_kd_m_ca1	mdo	kd	m	_
mdo_kd_f_ca1	mdo	kd	f	_
oan_kd_f_ca1	oan	kd	f	_

Previous module | Next module Module #295, TG: 2.4, TC: 2.4, 101 probes, 101 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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