Module #404, TG: 2.2, TC: 2.2, 108 probes, 108 Entrez genes, 7 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.

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-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.

regulation of cell communication

Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the 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.

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 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.

regulation of neurological system process

Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of neurological system.

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.

regulation of system process

Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system.

regulation of biological process

Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

regulation of cellular process

Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

regulation of synaptic transmission

Any process that modulates the frequency or rate of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.

regulation of multicellular organismal process

Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.

regulation of synaptic transmission, glutamatergic

Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.

regulation of transmission of nerve impulse

Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.

biological regulation

Any process that modulates the frequency, rate or extent of any biological process, quality or function.

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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.

regulation of cellular process

regulation of multicellular organismal process

regulation of biological process

cell-cell signaling

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

regulation of cell communication

transmission of nerve impulse

regulation of system process

Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system.

synaptic transmission

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

regulation of transmission of nerve impulse

transmission of nerve impulse

regulation of neurological system process

Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of neurological system.

regulation of synaptic transmission

Any process that modulates the frequency or rate of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.

regulation of transmission of nerve impulse

regulation of synaptic transmission, glutamatergic

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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.

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.

transmembrane transporter activity

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

glutamate receptor activity

Combining with glutamate to initiate a change in cell activity.

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.

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.

all

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.

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.

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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:0035249	1.159e-03	0.3115	5 CNR1, GRIA4, GRID2, GRIK1, GRM1	16	synaptic transmission, glutamatergic
GO:0007270	1.471e-03	0.5452	6 CNR1, GLRA1, GRIA4, GRID2, GRIK1, GRM1	28	nerve-nerve synaptic transmission
GO:0051966	3.772e-03	0.2142	4 CNR1, GRIA4, GRIK1, GRM1	11	regulation of synaptic transmission, glutamatergic
GO:0007268	7.968e-03	2.843	11	146	synaptic transmission
GO:0019226	1.705e-02	3.174	11	163	transmission of nerve impulse
GO:0006811	2.823e-02	6.464	16	332	ion transport
GO:0050877	4.419e-02	6.172	15	317	neurological system process
GO:0007215	4.575e-02	0.2142	3 GRIA4, GRID2, GRIK1	11	glutamate signaling pathway

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List of all enriched GO categories (cellular components), at the 0.05 p-value level.

The columns:

ExpCount is the expected count of genes in the module annotated with the given GO term, just by chance.
Count is the number of genes in the module annotated with the given GO term.
Size is the total number of genes (in our universe) annotated with the GO term.

Clicking on Count shows the genes that drive the enrichment. You can also click on the individual numbers in the Count column, to show the driving genes for that individual GO category.

Clicking on the GO identifiers takes you to the Gene Ontology web pages.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0016021	2.540e-02	31.58	46	1584	integral to membrane
GO:0031224	3.651e-02	32.24	46	1617	intrinsic to membrane
GO:0005887	4.172e-02	8.235	17	413	integral to plasma membrane
GO:0044456	4.192e-02	2.452	8	123	synapse part

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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:0015075	3.116e-03	5.719	17	300	ion transmembrane transporter activity
GO:0015276	4.232e-03	1.373	8	72	ligand-gated ion channel activity
GO:0022834	4.232e-03	1.373	8	72	ligand-gated channel activity
GO:0022836	5.902e-03	2.783	11	146	gated channel activity
GO:0008066	8.731e-03	0.286	4 GRIA4, GRID2, GRIK1, GRM1	15	glutamate receptor activity
GO:0022891	1.099e-02	6.52	17	342	substrate-specific transmembrane transporter activity
GO:0005416	1.702e-02	0.1525	3 SLC32A1, SLC6A11, SLC6A5	8	cation:amino acid symporter activity
GO:0015185	1.733e-02	0.03813	2 SLC32A1, SLC6A11	2	L-gamma-aminobutyric acid transmembrane transporter activity
GO:0005216	2.054e-02	3.355	11	176	ion channel activity
GO:0022857	2.113e-02	7.015	17	368	transmembrane transporter activity
GO:0022838	2.375e-02	3.431	11	180	substrate-specific channel activity
GO:0015267	3.139e-02	3.584	11	188	channel activity
GO:0022803	3.139e-02	3.584	11	188	passive transmembrane transporter activity
GO:0022892	3.344e-02	7.397	17	388	substrate-specific transporter activity
GO:0015187	3.870e-02	0.05719	2 SLC32A1, SLC6A5	3	glycine transmembrane transporter activity
GO:0005230	3.954e-02	0.8007	5 GABRR2, GLRA1, GRIA4, GRID2, GRIK1	42	extracellular ligand-gated ion channel 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	4.030e-02	1.723	7	102	Neuroactive ligand-receptor interaction
04730	4.580e-02	0.5066	4 C7orf16, GRID2, GRM1, PLCB4	30	Long-term depression

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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
mmu_cb_m2_ca1	mmu	cb	m	2
mmu_cb_m1_ca1	mmu	cb	m	1
gga_cb_m_ca1	gga	cb	m	_
mdo_cb_m_ca1	mdo	cb	m	_
gga_cb_f_ca1	gga	cb	f	_
mmu_cb_f_ca1	mmu	cb	f	_
mdo_cb_f_ca1	mdo	cb	f	_

Previous module | Next module Module #404, TG: 2.2, TC: 2.2, 108 probes, 108 Entrez genes, 7 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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