Module #285, TG: 3.6, TC: 1.2, 14 probes, 14 Entrez genes, 19 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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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.

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.

all

This term is the most general term possible

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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 centromere 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.

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 associated complex

Any multimeric complex connected to a microtubule.

microtubule cytoskeleton

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

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. 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 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 carbohydrate groups.

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.

cytoskeletal part

Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice.

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.

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.

organelle part

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

microtubule associated complex

Any multimeric complex connected to a microtubule.

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.

cytoskeletal part

microtubule associated complex

Any multimeric complex connected to a microtubule.

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.

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.

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.

all

This term is the most general term possible

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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:0007017	5.702e-03	0.2235	4 CENPE, KIF18B, KIF4A, TACC3	134	microtubule-based process
GO:0007018	1.084e-02	0.1001	3 CENPE, KIF18B, KIF4A	60	microtubule-based movement
GO:0030705	1.539e-02	0.1167	3 CENPE, KIF18B, KIF4A	70	cytoskeleton-dependent intracellular transport
GO:0007049	2.196e-02	1.077	6	646	cell cycle
GO:0006270	3.102e-02	0.03335	2 CDC45L, POLA1	20	DNA replication initiation
GO:0022403	4.823e-02	0.4753	4 AURKB, CENPE, POLA1, TACC3	285	cell cycle phase

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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:0044427	7.948e-04	0.3547	5 ASF1B, AURKB, CENPE, CENPI, POLA1	198	chromosomal part
GO:0005694	2.038e-03	0.4443	5 ASF1B, AURKB, CENPE, CENPI, POLA1	248	chromosome
GO:0043228	4.093e-03	2.399	9	1339	non-membrane-bounded organelle
GO:0043232	4.093e-03	2.399	9	1339	intracellular non-membrane-bounded organelle
GO:0015630	5.911e-03	0.5751	5 AURKB, CDC45L, CENPE, KIF18B, KIF4A	321	microtubule cytoskeleton
GO:0000775	6.021e-03	0.1129	3 AURKB, CENPE, CENPI	63	chromosome, centromeric region
GO:0005875	6.790e-03	0.1182	3 CENPE, KIF18B, KIF4A	66	microtubule associated complex
GO:0005819	1.098e-02	0.1433	3 AURKB, CENPE, KIF4A	80	spindle
GO:0044430	1.685e-02	0.7489	5 AURKB, CDC45L, CENPE, KIF18B, KIF4A	418	cytoskeletal part
GO:0044446	2.443e-02	4.796	11	2677	intracellular organelle part
GO:0044422	2.515e-02	4.814	11	2687	organelle part
GO:0016363	4.663e-02	0.06808	2 KIF4A, POLA1	38	nuclear matrix
GO:0005874	4.699e-02	0.2634	3 CENPE, KIF18B, KIF4A	147	microtubule

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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:0003777	4.032e-03	0.05822	3 CENPE, KIF18B, KIF4A	37	microtubule motor activity
GO:0003774	1.769e-02	0.1101	3 CENPE, KIF18B, KIF4A	70	motor 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-1515485851.cel	11	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485811.cel	9	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486351.cel	36	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486231.cel	30	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486271.cel	32	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486331.cel	35	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486291.cel	33	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485891.cel	13	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485651.cel	1	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-3860-raw-cel-1561690376.cel	13	5	HGPS	hgu133a	HGPS	AG11513
47B.CEL	4	3	DS-mosaic	hgu133plus2	Down mosaic	DS-mosaic 4
E-GEOD-3860-raw-cel-1561690336.cel	9	5	HGPS	hgu133a	HGPS	AG10750
E-GEOD-4219-raw-cel-1311956321.cel	9	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515486151.cel	26	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956614.cel	18	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-GEOD-3860-raw-cel-1561690472.cel	17	5	HGPS	hgu133a	none	GM00038C
46C.CEL	3	3	DS-mosaic	hgu133plus2	none	DS-mosaic 3
E-GEOD-3860-raw-cel-1561690344.cel	10	5	HGPS	hgu133a	none	GM00038C
E-GEOD-3860-raw-cel-1561690352.cel	11	5	HGPS	hgu133a	HGPS	AG11498

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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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