Module #22, TG: 2.8, TC: 2.6, 87 probes, 87 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.

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

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metabolic process

The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

generation of precursor metabolites and energy

The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

oxidation reduction

The process of removal or addition of one or more electrons with or without the concomitant removal or addition of a proton or protons.

respiratory electron transport chain

A process whereby a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.

oxidative phosphorylation

The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.

mitochondrial electron transport, NADH to ubiquinone

The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex I.

electron transport chain

A process whereby a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.

phosphorus metabolic process

The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).

phosphate metabolic process

The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.

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.

energy derivation by oxidation of organic compounds

The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.

phosphorylation

The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

ATP synthesis coupled electron transport

The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.

mitochondrial ATP synthesis coupled electron transport

The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP, as it occurs in the mitochondrial inner membrane or chloroplast thylakoid membrane.

cellular metabolic process

The chemical reactions and pathways by which individual cells transform chemical substances.

cellular respiration

The enzymatic release of energy from organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).

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cellular metabolic process

The chemical reactions and pathways by which individual cells transform chemical substances.

electron transport chain

ATP synthesis coupled electron transport

The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.

respiratory electron transport chain

oxidative phosphorylation

mitochondrial electron transport, NADH to ubiquinone

The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex I.

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

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

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

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

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intracellular

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

contractile fiber

Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.

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.

mitochondrion

A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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.

mitochondrial envelope

The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.

mitochondrial inner membrane

The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.

mitochondrial respiratory chain

The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

mitochondrial respiratory chain complex I

A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone.

organelle inner membrane

The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites.

myofibril

The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.

NADH dehydrogenase complex

An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone.

organelle membrane

The lipid bilayer surrounding an organelle.

mitochondrial membrane

Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.

organelle envelope

A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.

envelope

A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.

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.

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.

non-membrane-bounded organelle

Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.

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 non-membrane-bounded organelle

Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.

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.

organelle part

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

intracellular part

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

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.

mitochondrial part

Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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.

intracellular organelle part

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

mitochondrial membrane part

Any constituent part of a mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.

cell part

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

respiratory chain complex I

Respiratory chain complex I is an enzyme of the respiratory chain. It consists of at least 34 polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that projects into the matrix. The electrons of NADH enter the chain at this complex.

respiratory chain

The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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cell part

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

organelle part

organelle membrane

The lipid bilayer surrounding an organelle.

intracellular membrane-bounded organelle

intracellular non-membrane-bounded organelle

Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.

intracellular organelle part

organelle envelope

A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.

intracellular part

organelle membrane

The lipid bilayer surrounding an organelle.

membrane part

organelle envelope

A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.

organelle inner membrane

The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites.

NADH dehydrogenase complex

intracellular organelle

intracellular organelle part

NADH dehydrogenase complex

organelle inner membrane

The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites.

mitochondrial inner membrane

The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.

mitochondrial membrane part

Any constituent part of a mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.

mitochondrial envelope

The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.

mitochondrial membrane

Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.

mitochondrial membrane part

Any constituent part of a mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.

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.

contractile fiber

Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.

mitochondrion

A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

mitochondrial part

mitochondrial respiratory chain

respiratory chain complex I

mitochondrial respiratory chain complex I

mitochondrial membrane

Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.

mitochondrial part

mitochondrial respiratory chain

mitochondrial respiratory chain complex I

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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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electron carrier activity

Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system.

molecular_function

Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.

catalytic activity

Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

NADH dehydrogenase activity

Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.

oxidoreductase activity

Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

NADH dehydrogenase (ubiquinone) activity

Catalysis of the reaction: NADH + H+ + ubiquinone = NAD+ + ubiquinol.

oxidoreductase activity, acting on NADH or NADPH

Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor

Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.

NADH dehydrogenase (quinone) activity

Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol.

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NADH dehydrogenase (quinone) activity

Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol.

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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:0022900	7.097e-04	0.5079	6	76	electron transport chain
GO:0006120	1.238e-03	0.1671	4 DLD, NDUFA8, NDUFS1, NDUFS3	25	mitochondrial electron transport, NADH to ubiquinone
GO:0042773	3.523e-03	0.2272	4 DLD, NDUFA8, NDUFS1, NDUFS3	34	ATP synthesis coupled electron transport
GO:0042775	3.523e-03	0.2272	4 DLD, NDUFA8, NDUFS1, NDUFS3	34	mitochondrial ATP synthesis coupled electron transport
GO:0006119	3.607e-03	0.441	5 DLD, NDUFA8, NDUFS1, NDUFS3, UQCRC2	66	oxidative phosphorylation
GO:0045333	3.842e-03	0.4477	5 DLD, NDUFA8, NDUFS1, NDUFS3, UQCRC2	67	cellular respiration
GO:0015980	4.897e-03	0.7618	6	114	energy derivation by oxidation of organic compounds
GO:0022904	6.018e-03	0.2673	4 DLD, NDUFA8, NDUFS1, NDUFS3	40	respiratory electron transport chain
GO:0008053	1.002e-02	0.02673	2 MFN1, MFN2	4	mitochondrial fusion
GO:0055114	2.574e-02	3.081	10	461	oxidation reduction
GO:0006091	2.826e-02	1.597	7	239	generation of precursor metabolites and energy
GO:0006086	3.769e-02	0.06014	2 DLD, PDHX	9	acetyl-CoA biosynthetic process from pyruvate
GO:0010510	3.769e-02	0.06014	2 DLD, PDHX	9	regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0051193	4.423e-02	0.06682	2 DLD, PDHX	10	regulation of cofactor metabolic process
GO:0051196	4.423e-02	0.06682	2 DLD, PDHX	10	regulation of coenzyme metabolic process

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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:0044429	7.744e-06	2.595	14	430	mitochondrial part
GO:0005740	4.338e-05	1.792	11	297	mitochondrial envelope
GO:0005746	8.295e-05	0.2293	5 NDUFA12, NDUFA8, NDUFS1, NDUFS3, UQCRC2	38	mitochondrial respiratory chain
GO:0044455	1.190e-04	0.4345	6	72	mitochondrial membrane part
GO:0070469	1.319e-04	0.2534	5 NDUFA12, NDUFA8, NDUFS1, NDUFS3, UQCRC2	42	respiratory chain
GO:0031966	1.542e-04	1.677	10	278	mitochondrial membrane
GO:0005747	4.421e-04	0.1629	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	27	mitochondrial respiratory chain complex I
GO:0030964	4.421e-04	0.1629	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	27	NADH dehydrogenase complex
GO:0045271	4.421e-04	0.1629	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	27	respiratory chain complex I
GO:0031975	5.367e-04	2.872	12	476	envelope
GO:0031967	1.811e-03	2.806	11	465	organelle envelope
GO:0005739	1.901e-03	5.618	16	931	mitochondrion
GO:0030016	2.867e-03	0.5189	5 ANKRD1, CSRP3, LRRC10, MYOZ2, MYPN	86	myofibril
GO:0043292	4.113e-03	0.5672	5 ANKRD1, CSRP3, LRRC10, MYOZ2, MYPN	94	contractile fiber
GO:0030017	1.349e-02	0.4465	4 ANKRD1, CSRP3, MYOZ2, MYPN	74	sarcomere
GO:0019867	1.721e-02	0.4827	4 MFN1, MFN2, P2RX1, VDAC3	80	outer membrane
GO:0005743	1.735e-02	1.225	6	203	mitochondrial inner membrane
GO:0044449	2.142e-02	0.5189	4 ANKRD1, CSRP3, MYOZ2, MYPN	86	contractile fiber part
GO:0019866	2.478e-02	1.334	6	221	organelle inner membrane
GO:0031674	2.541e-02	0.2595	3 ANKRD1, CSRP3, MYOZ2	43	I band

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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:0016651	1.295e-04	0.3816	6	58	oxidoreductase activity, acting on NADH or NADPH
GO:0003954	1.074e-03	0.1711	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	26	NADH dehydrogenase activity
GO:0008137	1.074e-03	0.1711	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	26	NADH dehydrogenase (ubiquinone) activity
GO:0050136	1.074e-03	0.1711	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	26	NADH dehydrogenase (quinone) activity
GO:0009055	1.571e-03	0.625	6 DLD, ME2, NDUFA12, NDUFS1, NDUFS3, NOX3	95	electron carrier activity
GO:0016655	1.576e-03	0.1908	4 NDUFA12, NDUFA8, NDUFS1, NDUFS3	29	oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor
GO:0051287	4.097e-02	0.2566	3 DLD, ME2, SIRT5	39	NAD or NADH binding

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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
05012	2.108e-03	0.4505	5 NDUFA8, NDUFS1, NDUFS3, UQCRC2, VDAC3	72	Parkinson's disease
05016	1.075e-02	0.682	5 NDUFA8, NDUFS1, NDUFS3, UQCRC2, VDAC3	109	Huntington's disease
00190	2.249e-02	0.4755	4 NDUFA8, NDUFS1, NDUFS3, UQCRC2	76	Oxidative phosphorylation

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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
ppa_ht_f_ca1	ppa	ht	f	_
ppy_ht_m_ca1	ppy	ht	m	_
ptr_ht_m_ca1	ptr	ht	m	_

Previous module | Next module Module #22, TG: 2.8, TC: 2.6, 87 probes, 87 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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