Module #539, TG: 2, TC: 1.2, 143 probes, 142 Entrez genes, 20 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.

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

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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.

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.

cell communication

Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

cell surface receptor linked signaling pathway

Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell.

G-protein coupled receptor protein signaling pathway

The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.

gamma-aminobutyric acid signaling pathway

The series of molecular signals generated by the binding of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to a cell surface receptor.

cell-cell signaling

Any process that mediates the transfer of information from one cell to another.

synaptic transmission

The process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.

nerve-nerve synaptic transmission

The process of communication from a neuron to another neuron across a synapse.

neurological system process

A organ system process carried out by any of the organs or tissues of neurological system.

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.

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.

transmission of nerve impulse

The neurological system process by which a signal is transmitted through the nervous system by synaptic transmission and the sequential electrochemical polarization and depolarization that travels across the membrane of a nerve cell (neuron) in response to stimulation.

signaling pathway

The series of molecular events whereby information is sent from one location to another within a living organism or between living organisms.

signaling process

Any biological process involved in the generation, transmission, reception, or interpretation of a signal. A signal is an entity used to transmit or convey information.

signaling

The entirety of a process whereby information is transmitted. This process begins with the initiation of the signal and ends when a response has been triggered.

signal transmission

The process whereby a signal is released and/or conveyed from one location to another.

multicellular organismal process

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

synaptic transmission, glutamatergic

The process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.

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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signaling process

Any biological process involved in the generation, transmission, reception, or interpretation of a signal. A signal is an entity used to transmit or convey information.

establishment of localization

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

cell-cell signaling

Any process that mediates the transfer of information from one cell to another.

transmission of nerve impulse

synaptic transmission

The process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.

transmission of nerve impulse

HELP

This is one of three sections showing Gene Ontology enrichment of the current module: in this case for cellular components.

Move the mouse cursor over the terms to get their definition. Clicking on them takes you to the corresponding Gene Ontology web page.

If you cannot see a graph here at all, that means that there were no significantly enriched GO categories, at the 0.05 level.

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

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plasma membrane

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

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.

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.

integral to plasma membrane

Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer.

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.

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.

intrinsic to plasma membrane

Located in the plasma 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.

macromolecular complex

A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.

ion channel complex

A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.

protein complex

Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.

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.

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 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.

membrane part

ion channel complex

A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.

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.

intrinsic to plasma membrane

ion channel complex

A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.

integral to plasma membrane

Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer.

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.

signal transducer activity

Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell.

receptor activity

Combining with an extracellular or intracellular messenger to initiate a change in cell activity.

transmembrane receptor activity

Combining with an extracellular or intracellular messenger to initiate a change in cell activity, and spanning to the membrane of either the cell or an organelle.

transporter activity

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

ion channel activity

Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.

extracellular ligand-gated ion channel activity

Catalysis of the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts.

cation channel activity

Catalysis of the energy-independent passage of cations across a lipid bilayer down a concentration gradient.

calcium channel activity

Catalysis of facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.

transmembrane transporter activity

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

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.

channel activity

Catalysis of energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.

ligand-gated ion channel activity

Catalysis of the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.

store-operated calcium channel activity

A ligand-gated ion channel activity which transports calcium in response to emptying of intracellular calcium stores.

passive transmembrane transporter activity

Catalysis of the transfer of a solute from one side of the membrane to the other, down the solute's concentration gradient.

ligand-gated channel activity

Catalysis of the transmembrane transfer of a solute by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.

gated channel activity

Catalysis of the transmembrane transfer of a solute by a channel that opens in response to a specific stimulus.

substrate-specific channel activity

Catalysis of energy-independent facilitated diffusion, mediated by passage of a specific solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.

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.

molecular transducer activity

The molecular function that accepts an input of one form and creates an output of a different form.

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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.

substrate-specific channel activity

ion channel activity

Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.

cation channel activity

Catalysis of the energy-independent passage of cations across a lipid bilayer down a concentration gradient.

ligand-gated ion channel activity

Catalysis of the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.

store-operated calcium channel activity

A ligand-gated ion channel activity which transports calcium in response to emptying of intracellular calcium stores.

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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:0019226	3.194e-05	4.207	18	163	transmission of nerve impulse
GO:0007268	3.375e-05	3.768	17	146	synaptic transmission
GO:0006811	1.339e-04	8.569	25	332	ion transport
GO:0007270	6.753e-04	0.7227	7	28	nerve-nerve synaptic transmission
GO:0035249	3.520e-03	0.4129	5 CACNB4, CNR1, GRIA4, GRID2, GRM1	16	synaptic transmission, glutamatergic
GO:0006810	3.598e-03	27.64	47	1071	transport
GO:0050877	4.102e-03	8.182	21	317	neurological system process
GO:0007214	4.375e-03	0.2323	4 CACNB4, GABRA2, GABRA4, GABRB2	9	gamma-aminobutyric acid signaling pathway
GO:0051234	4.582e-03	27.95	47	1083	establishment of localization
GO:0007267	1.360e-02	7.123	18	276	cell-cell signaling
GO:0003008	1.709e-02	11.38	24	441	system process
GO:0050801	2.159e-02	4.388	13	170	ion homeostasis
GO:0007186	2.644e-02	4.517	13	175	G-protein coupled receptor protein signaling pathway
GO:0042391	2.729e-02	1.445	7	56	regulation of membrane potential
GO:0006873	2.922e-02	4	12	155	cellular ion homeostasis
GO:0055082	3.177e-02	4.052	12	157	cellular chemical homeostasis
GO:0006812	3.280e-02	5.885	15	228	cation transport
GO:0051969	3.732e-02	1.549	7	60	regulation of transmission of nerve impulse
GO:0031644	4.017e-02	1.574	7	61	regulation of neurological system process
GO:0051179	4.490e-02	32.36	48	1254	localization
GO:0006816	4.773e-02	2.116	8	82	calcium ion transport

HELP

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:0016020	1.879e-09	60.6	98	2327	membrane
GO:0031224	2.613e-08	42.11	77	1617	intrinsic to membrane
GO:0044425	1.651e-07	49.46	83	1899	membrane part
GO:0016021	5.053e-07	41.25	73	1584	integral to membrane
GO:0005886	2.225e-05	29.51	55	1133	plasma membrane
GO:0044459	1.597e-03	18.78	36	721	plasma membrane part
GO:0005887	7.640e-03	10.76	23	413	integral to plasma membrane
GO:0034702	9.563e-03	2.813	10	108	ion channel complex
GO:0031226	9.998e-03	11.02	23	423	intrinsic to plasma membrane
GO:0034707	1.151e-02	0.7032	5 ANO3, GABRA2, GABRA4, GABRB2, GLRA1	27	chloride channel complex
GO:0032281	1.325e-02	0.05209	2 GRIA1, GRIA4	2	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex
GO:0045202	1.589e-02	4.167	12	160	synapse
GO:0044456	2.161e-02	3.203	10	123	synapse part
GO:0016023	2.625e-02	6.38	15	245	cytoplasmic membrane-bounded vesicle
GO:0031264	3.136e-02	0.07813	2 FADD, RIPK1	3	death-inducing signaling complex
GO:0031988	3.177e-02	6.537	15	251	membrane-bounded vesicle
GO:0031410	4.216e-02	6.797	15	261	cytoplasmic vesicle
GO:0045211	4.684e-02	1.979	7	76	postsynaptic membrane

HELP

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:0015075	9.844e-05	7.753	24	300	ion transmembrane transporter activity
GO:0022891	2.282e-04	8.838	25	342	substrate-specific transmembrane transporter activity
GO:0015276	2.830e-04	1.861	11	72	ligand-gated ion channel activity
GO:0022834	2.830e-04	1.861	11	72	ligand-gated channel activity
GO:0022836	5.387e-04	3.773	15	146	gated channel activity
GO:0022857	6.419e-04	9.51	25	368	transmembrane transporter activity
GO:0005216	1.034e-03	4.548	16	176	ion channel activity
GO:0022838	1.306e-03	4.652	16	180	substrate-specific channel activity
GO:0022892	1.363e-03	10.03	25	388	substrate-specific transporter activity
GO:0015267	2.014e-03	4.858	16	188	channel activity
GO:0022803	2.014e-03	4.858	16	188	passive transmembrane transporter activity
GO:0005215	2.215e-03	11.73	27	454	transporter activity
GO:0005230	5.696e-03	1.085	7	42	extracellular ligand-gated ion channel activity
GO:0015279	9.550e-03	0.1292	3 TRPC1, TRPC3, TRPC5	5	store-operated calcium channel activity
GO:0004888	9.961e-03	7.003	18	271	transmembrane receptor activity
GO:0008509	1.255e-02	1.68	8	65	anion transmembrane transporter activity
GO:0005254	1.763e-02	0.982	6	38	chloride channel activity
GO:0005253	1.963e-02	1.008	6	39	anion channel activity
GO:0008066	2.098e-02	0.3876	4 GRIA1, GRIA4, GRID2, GRM1	15	glutamate receptor activity
GO:0005003	2.371e-02	0.1809	3 EPHA3, EPHA5, EPHA8	7	ephrin receptor activity
GO:0015185	2.750e-02	0.05168	2 SLC32A1, SLC6A11	2	L-gamma-aminobutyric acid transmembrane transporter activity
GO:0005416	3.334e-02	0.2067	3 SLC32A1, SLC6A11, SLC6A9	8	cation:amino acid symporter activity
GO:0042165	3.451e-02	0.7753	5 GABRA2, GABRA4, GPR139, NPY5R, SLC6A11	30	neurotransmitter binding
GO:0004872	4.375e-02	10.39	21	402	receptor activity
GO:0005275	4.694e-02	0.8528	5	33	amine 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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Id	Pvalue	ExpCount	Count	Size	Term
04080	8.708e-03	2.584	10	102	Neuroactive ligand-receptor interaction
00601	2.263e-02	0.1773	3 B3GALT5, B4GALT1, FUT9	7	Glycosphingolipid biosynthesis - lacto and neolacto series

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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
hsa_lv_m2_ca1	hsa	lv	m	2
hsa_lv_m1_ca1	hsa	lv	m	1
mmu_cb_m2_ca1	mmu	cb	m	2
mdo_br_m_ca1	mdo	br	m	_
mmu_br_m2_ca1	mmu	br	m	2
mmu_cb_m1_ca1	mmu	cb	m	1
mmu_cb_f_ca1	mmu	cb	f	_
mdo_cb_m_ca1	mdo	cb	m	_
mmu_br_m1_ca1	mmu	br	m	1
mmu_br_f_ca1	mmu	br	f	_
mdo_cb_f_ca1	mdo	cb	f	_
gga_cb_m_ca1	gga	cb	m	_
mdo_br_f_ca1	mdo	br	f	_
gga_cb_f_ca1	gga	cb	f	_
oan_cb_m_ca1	oan	cb	m	_
oan_br_f_ca1	oan	br	f	_
oan_cb_f_ca1	oan	cb	f	_
gga_br_m_ca1	gga	br	m	_
gga_br_f_ca1	gga	br	f	_
oan_br_m_ca1	oan	br	m	_

Previous module | Next module Module #539, TG: 2, TC: 1.2, 143 probes, 142 Entrez genes, 20 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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