Module #272, TG: 2.4, TC: 2.6, 100 probes, 98 Entrez genes, 4 conditions

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Under-expression is coded with green, over-expression with red color.

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

The graph shows the hierarchy of the GO categories, their enrichment for the current module is color coded, and the blue number beside the category is the minus log ten p-value of the enrichment. (Calculated using the standard hypergeometric test.) The color of the arrows code «is a» (cyan) and «part of» relationships.

The tree was built the following way. First all GO terms with more significant enrichment p-value than 0.05 were collected. Then all paths from these terms to the root node of the GO tree were included too. If a GO term is included more than once in the tree, then the green numbers show 1) the id of the node, this makes it easier to find other appereances of the term, and 2) the number of appearences.

Note that the same GO category might show up on the graph many times. This is because the GO was «straightened» for this graph, i.e. if there are more paths from a GO term to the root node of the tree, all of them are included. The green numbers

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

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

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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.

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.

nitrogen compound metabolic process

The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds; includes nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium.

microtubule-based process

Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.

microtubule-based movement

Movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins.

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.

cellular nitrogen compound metabolic process

The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.

cellular metabolic process

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

primary metabolic process

The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.

nucleic acid metabolic process

Any cellular metabolic process involving nucleic acids.

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cellular metabolic process

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

cellular nitrogen compound metabolic process

The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.

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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.

chromosome, centromeric region

The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.

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.

nucleus

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

chromosome

A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

cytoskeleton

Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

microtubule cytoskeleton

The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.

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.

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.

chromosomal part

Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

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.

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.

organelle part

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

intracellular part

intracellular organelle

intracellular organelle part

chromosomal part

Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

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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.

nucleic acid binding

Interacting selectively and non-covalently with any nucleic acid.

DNA binding

Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).

chromatin binding

Interacting selectively and non-covalently with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase.

motor activity

Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate.

microtubule motor activity

Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).

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.

nucleoside-triphosphatase activity

Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.

binding

The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.

pyrophosphatase activity

Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.

hydrolase activity

Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

hydrolase activity, acting on acid anhydrides

Catalysis of the hydrolysis of any acid anhydride.

hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides

Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.

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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:0007018	2.839e-03	0.6176	6	44	microtubule-based movement
GO:0090304	7.120e-03	15.09	29	1075	nucleic acid metabolic process
GO:0007017	7.259e-03	1.474	8	105	microtubule-based process
GO:0006355	1.137e-02	6.583	17	469	regulation of transcription, DNA-dependent
GO:0051252	1.573e-02	6.808	17	485	regulation of RNA metabolic process
GO:0006351	2.680e-02	7.229	17	515	transcription, DNA-dependent
GO:0048610	2.766e-02	1.039	6	74	reproductive cellular process
GO:0032774	2.770e-02	7.257	17	517	RNA biosynthetic process
GO:0006259	2.898e-02	2.934	10	209	DNA metabolic process
GO:0045132	2.955e-02	0.04211	2 SGOL1, STRA8	3	meiotic chromosome segregation
GO:0048645	4.614e-02	0.2106	3 GLI3, TLX1, TP63	15	organ formation
GO:0006266	4.849e-02	0.05615	2 APTX, TOP2A	4	DNA ligation

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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:0005694	7.307e-05	2.197	12	150	chromosome
GO:0044427	7.564e-05	1.816	11	124	chromosomal part
GO:0000775	4.396e-04	0.791	7	54	chromosome, centromeric region
GO:0015630	2.619e-03	3.325	12	227	microtubule cytoskeleton
GO:0005634	2.685e-03	22.38	38	1528	nucleus
GO:0044424	2.319e-02	51.89	63	3542	intracellular part
GO:0043228	2.883e-02	12.52	23	855	non-membrane-bounded organelle
GO:0043232	2.883e-02	12.52	23	855	intracellular non-membrane-bounded organelle
GO:0044430	4.337e-02	4.907	12	335	cytoskeletal part
GO:0044446	4.757e-02	24.48	36	1671	intracellular organelle 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.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0003682	2.612e-04	0.8536	8	65	chromatin binding
GO:0003677	2.378e-03	6.947	19	529	DNA binding
GO:0003676	2.884e-03	10.53	24	802	nucleic acid binding
GO:0003777	3.034e-03	0.394	5 KIF14, KIF18B, KIF24, KIF27, KIF2B	30	microtubule motor activity
GO:0030528	1.819e-02	3.9	12	297	transcription regulator activity
GO:0003774	2.853e-02	0.7223	5 KIF14, KIF18B, KIF24, KIF27, KIF2B	55	motor activity
GO:0043565	3.949e-02	2.64	9	201	sequence-specific DNA binding
GO:0003700	4.143e-02	3.809	11	290	sequence-specific DNA binding transcription factor activity

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List of all enriched KEGG pathways, at the 0.05 p-value level.

The columns:

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

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

Clicking on the KEGG identifiers takes you to the KEGG web site.

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List of all enriched miRNA families, at the 0.05 p-value level.

The columns:

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

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

The miRNA regulation data was taken from the TargetScan database. (Only the conserved sites were used for the current analysis.) Clicking on the miRNA names takes you to the TargetScan web site.

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List of all enriched Chromosomes, at the 0.05 p-value level.

The columns:

ExpCount is the expected number of genes in the module on the given chromosome, just by chance.
Count is the number of genes in the module on the given chromosome.
Size is the total number of genes (in our universe) on the given chromosome.

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

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A list of all genes in the current module, in alphabetical order. The size of the text corresponds to the gene scores.

Text color indicates correlation and anti-correlation: genes of the same color are correlated, both move up or down in the module samples (listed below). Genes of different color are anti-correlated, they have opposite behavior in the module samples.

Note, that text color of the individual genes should be interpreted together with the coloring of the samples below. For red samples, red genes have a higher expression (compared to the average gene expression level), green genes have a lower expression.

Green samples have opposite behavior, in these red genes have a lower expression, green genes have a higher expression.

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

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

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

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

The height of each bar corresponds to the weighted mean expression of the module genes. The weights are the gene scores of the module and they are positive for the genes listed in red above and they are negative for the genes that are listed in green.

Bars going up correspond to samples listed in red (the ones that are different enough to included in the module). In these samples the red module genes are highly expressed, and the green module genes are lowly expressed. The behavior of the genes is the opposite for bars going down.

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

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

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Id	species	tissue	sex	individual
gga_ts_m2_ca1	gga	ts	m	2
gga_ts_m1_ca1	gga	ts	m	1
mdo_ts_m1_ca1	mdo	ts	m	1
mdo_ts_m2_ca1	mdo	ts	m	2

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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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