Module #115, TG: 3.8, TC: 2, 20 probes, 20 Entrez genes, 3 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.

transport

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism.

dicarboxylic acid transport

The directed movement of dicarboxylic acids into, out of, within or between cells.

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.

organic acid transport

The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of, within or between cells.

multicellular organismal process

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

carboxylic acid transport

The directed movement of carboxylic acids into, out of, within or between cells. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).

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.

all

This term is the most general term possible

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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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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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.

presynaptic membrane

A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

synapse part

Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.

cell part

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

synapse

The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

all

This term is the most general term possible

cell part

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

synapse part

Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.

presynaptic membrane

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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

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

dicarboxylic acid transmembrane transporter activity

Catalysis of the transfer of dicarboxylic acids from one side of the membrane to the other. A dicarboxylic acid is an organic acid with two COOH groups.

organic acid:sodium symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: organic acid(out) + Na+(out) = organic acid(in) + Na+(in).

organic acid transmembrane transporter activity

Catalysis of the transfer of organic acids, any acidic compound containing carbon in covalent linkage, from one side of the 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.

anion transmembrane transporter activity

Catalysis of the transfer of a negatively charged ion from one side of a 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.

solute:cation symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + cation(out) = solute(in) + cation(in).

anion:cation symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(out) + cation(out) = anion(in) + cation(in).

solute:sodium symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + Na+(out) = solute(in) + Na+(in).

sodium:dicarboxylate symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: dicarboxylate(out) + Na+(out) = dicarboxylate(in) + Na+(in).

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.

substrate-specific transmembrane transporter activity

Catalysis of 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.

carboxylic acid transmembrane transporter activity

Catalysis of the transfer of carboxylic acids from one side of the membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).

all

This term is the most general term possible

substrate-specific transmembrane transporter activity

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

solute:cation symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + cation(out) = solute(in) + cation(in).

anion:cation symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(out) + cation(out) = anion(in) + cation(in).

sodium:dicarboxylate symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: dicarboxylate(out) + Na+(out) = dicarboxylate(in) + Na+(in).

sodium:dicarboxylate symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: dicarboxylate(out) + Na+(out) = dicarboxylate(in) + Na+(in).

organic acid:sodium symporter activity

Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: organic acid(out) + Na+(out) = organic acid(in) + Na+(in).

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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:0006835	6.429e-03	0.01251	2 SLC1A2, SLC1A7	5	dicarboxylic acid transport
GO:0050877	8.424e-03	0.7929	6 AGT, DSPP, NDP, SLC1A2, SYT1, TULP2	317	neurological system process
GO:0007417	3.102e-02	0.3827	4 AGT, LRP2, NRCAM, SLC1A2	153	central nervous system development
GO:0003008	3.327e-02	1.113	6 AGT, DSPP, NDP, SLC1A2, SYT1, TULP2	445	system process
GO:0001890	4.664e-02	0.04503	2 HAND1, NDP	18	placenta development

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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:0042734	1.871e-03	0.01088	2 SLC1A2, SYT1	5	presynaptic membrane
GO:0043005	1.090e-02	0.1414	3 NRCAM, SLC1A2, SYT1	65	neuron projection
GO:0030139	2.492e-02	0.04569	2 LRP2, SYT1	21	endocytic vesicle
GO:0042995	3.519e-02	0.5134	4 LRP2, NRCAM, SLC1A2, SYT1	236	cell projection
GO:0016013	4.941e-02	0.002176	1 SNTG1	1	syntrophin complex

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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:0005310	7.026e-03	0.01115	2 SLC1A2, SLC1A7	5	dicarboxylic acid transmembrane transporter activity
GO:0017153	7.026e-03	0.01115	2 SLC1A2, SLC1A7	5	sodium:dicarboxylate symporter activity
GO:0005313	1.561e-02	0.01783	2 SLC1A2, SLC1A7	8	L-glutamate transmembrane transporter activity
GO:0015172	1.561e-02	0.01783	2 SLC1A2, SLC1A7	8	acidic amino acid transmembrane transporter activity
GO:0005343	2.185e-02	0.02229	2 SLC1A2, SLC1A7	10	organic acid:sodium symporter activity
GO:0015296	4.341e-02	0.03567	2 SLC1A2, SLC1A7	16	anion:cation symporter activity
GO:0015370	4.341e-02	0.03567	2 SLC1A2, SLC1A7	16	solute:sodium symporter 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.

Note that some gene symbols may show up more than once, if many probes match the same Entrez gene.

Genes with no Entrez mapping are given separately, with their Affymetrics probe ID.

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Conditions in the module, given in the same order as on the expression plot above. Red color means over-expression, green under-expression in the given condition.

The barplot below shows the condition (sample) scores. A separate bar is shown for each sample, its height is the corresponding score of the sample in the module. The red and green numbers on the bars are the sample scores expressed in percents, i.e. 100% is 1.0.

The red and green lines show the module thresholds, samples above the red line and below the green line are included in the module.

The different experiments that were part of the study, are separated by dashed vertical lines.

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Id	sample	Experiment	ExpName	Array	Syndrome	Cell.line
E-TABM-263-raw-cel-1515485711.cel	4	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485951.cel	16	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486311.cel	34	6	Cycle	hgu133a2	none	Cycle 1

Previous module | Next module Module #115, TG: 3.8, TC: 2, 20 probes, 20 Entrez genes, 3 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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