Module #347, TG: 2.2, TC: 3, 194 probes, 191 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.

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

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reproduction

The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.

chromosome segregation

The process by which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets.

M phase of mitotic cell cycle

A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the mitotic cell cycle during which mitosis takes place.

microtubule cytoskeleton organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.

mitotic cell cycle

Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.

M phase

A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the cell cycle comprising nuclear division.

nuclear division

A process by which a cell nucleus is divided into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.

reproductive developmental process

A developmental process by which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.

cytoskeleton organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.

organelle organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

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.

cell cycle

The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.

mitosis

A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.

meiosis

A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations.

gamete generation

The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.

germ cell development

The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.

spermatogenesis

The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.

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.

fertilization

The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).

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 component organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.

sexual reproduction

The regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.

cell cycle process

A cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.

cell cycle phase

A cell cycle process comprising the steps by which a cell progresses through one of the biochemical and morphological phases and events that occur during successive cell replication or nuclear replication events.

reproductive process

A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

cell differentiation

The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.

multicellular organismal process

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

developmental process

A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.

multicellular organism reproduction

The biological process by which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

male gamete generation

Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction.

organelle fission

The creation of two or more organelles by division of one organelle.

cell development

The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.

reproductive process in a multicellular organism

The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.

reproductive cellular process

A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular or single-celled organism.

anatomical structure development

The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.

cellular developmental process

A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.

meiotic cell cycle

Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell.

M phase of meiotic cell cycle

A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the meiotic cell cycle during which meiosis takes place.

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reproductive process

organelle organization

reproductive cellular process

A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular or single-celled organism.

multicellular organism reproduction

The biological process by which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.

reproductive process in a multicellular organism

The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.

reproductive developmental process

A developmental process by which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.

cellular developmental process

A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.

fertilization

The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).

reproductive process in a multicellular organism

The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.

cell cycle process

A cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.

germ cell development

gamete generation

The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.

cell development

germ cell development

microtubule cytoskeleton organization

cell development

germ cell development

mitosis

meiosis

M phase of mitotic cell cycle

A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the mitotic cell cycle during which mitosis takes place.

M phase of meiotic cell cycle

A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the meiotic cell cycle during which meiosis takes place.

HELP

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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condensed chromosome

A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.

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.

ribonucleoprotein complex

A macromolecular complex containing both protein and RNA molecules.

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.

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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

Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

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.

chromatoid body

A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182).

P granule

A small cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.

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.

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.

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.

cell part

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

pole plasm

Differentiated cytoplasm associated with a pole (animal, vegetal, anterior, or posterior) of an oocyte, egg or early embryo.

germ plasm

Differentiated cytoplasm associated with a pole of an oocyte, egg or early embryo that will be inherited by the cells that will give rise to the germ line.

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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

ribonucleoprotein complex

A macromolecular complex containing both protein and RNA molecules.

intracellular organelle

intracellular organelle part

microtubule

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.

P granule

A small cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.

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

P granule

A small cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.

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.

nucleic acid binding

Interacting selectively and non-covalently with any nucleic acid.

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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HELP

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.

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

Id	Pvalue	ExpCount	Count	Size	Term
GO:0000279	2.713e-08	4.026	22	152	M phase
GO:0022403	1.665e-07	5.351	24	202	cell cycle phase
GO:0022402	2.094e-07	6.861	27	259	cell cycle process
GO:0007126	8.507e-07	1.245	12	47	meiosis
GO:0051321	8.507e-07	1.245	12	47	meiotic cell cycle
GO:0051327	8.507e-07	1.245	12	47	M phase of meiotic cell cycle
GO:0007049	1.441e-06	9.801	31	370	cell cycle
GO:0007017	9.923e-05	2.781	14	105	microtubule-based process
GO:0007283	1.260e-04	2.437	13	92	spermatogenesis
GO:0048232	1.260e-04	2.437	13	92	male gamete generation
GO:0007059	3.926e-04	0.9271	8	35	chromosome segregation
GO:0048610	4.442e-04	1.96	11	74	reproductive cellular process
GO:0019953	6.726e-04	3.841	15	145	sexual reproduction
GO:0000278	1.943e-03	4.794	16	181	mitotic cell cycle
GO:0000280	2.182e-03	2.834	12	107	nuclear division
GO:0007067	2.182e-03	2.834	12	107	mitosis
GO:0000087	2.359e-03	2.861	12	108	M phase of mitotic cell cycle
GO:0007276	2.893e-03	3.417	13	129	gamete generation
GO:0048285	3.168e-03	2.967	12	112	organelle fission
GO:0007281	3.310e-03	0.9536	7	36	germ cell development
GO:0022414	3.514e-03	7.443	20	281	reproductive process
GO:0000003	3.656e-03	7.47	20	282	reproduction
GO:0000226	6.488e-03	1.854	9	70	microtubule cytoskeleton organization
GO:0009566	8.026e-03	0.5033	5 FNDC3A, KLHL10, STRA8, ZPBP, ZPBP2	19	fertilization
GO:0007018	9.590e-03	1.165	7	44	microtubule-based movement
GO:0032504	1.118e-02	4.583	14	173	multicellular organism reproduction
GO:0048609	1.118e-02	4.583	14	173	reproductive process in a multicellular organism
GO:0006259	2.048e-02	5.536	15	209	DNA metabolic process
GO:0031047	2.190e-02	0.3708	4 LIN28B, NCBP1, PIWIL1, TDRD1	14	gene silencing by RNA
GO:0051301	2.676e-02	3.947	12	149	cell division
GO:0016458	3.063e-02	0.7152	5 HELLS, LIN28B, NCBP1, PIWIL1, TDRD1	27	gene silencing
GO:0051276	3.480e-02	4.106	12	155	chromosome organization
GO:0030261	4.164e-02	0.2119	3 NCAPG, STRA8, TOP2A	8	chromosome condensation
GO:0006323	4.648e-02	0.4768	4 HELLS, NCAPG, STRA8, TOP2A	18	DNA packaging

HELP

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:0005634	3.136e-06	41.04	71	1528	nucleus
GO:0005694	2.443e-05	4.028	17	150	chromosome
GO:0043228	4.556e-05	22.96	46	855	non-membrane-bounded organelle
GO:0043232	4.556e-05	22.96	46	855	intracellular non-membrane-bounded organelle
GO:0044427	2.073e-04	3.33	14	124	chromosomal part
GO:0015630	9.968e-04	6.096	18	227	microtubule cytoskeleton
GO:0000775	2.353e-03	1.45	8	54	chromosome, centromeric region
GO:0005874	3.451e-03	2.901	11	108	microtubule
GO:0044424	3.873e-03	95.13	113	3542	intracellular part
GO:0005622	4.249e-03	97.76	115	3640	intracellular
GO:0000793	6.757e-03	1.316	7	49	condensed chromosome
GO:0033391	7.993e-03	0.1611	3 PIWIL1, TDRD1, TDRD6	6	chromatoid body
GO:0043186	7.993e-03	0.1611	3 PIWIL1, TDRD1, TDRD6	6	P granule
GO:0045495	7.993e-03	0.1611	3 PIWIL1, TDRD1, TDRD6	6	pole plasm
GO:0060293	7.993e-03	0.1611	3 PIWIL1, TDRD1, TDRD6	6	germ plasm
GO:0043234	8.491e-03	25.57	42	952	protein complex
GO:0032991	1.102e-02	28.49	45	1061	macromolecular complex
GO:0043229	1.876e-02	79.82	97	2972	intracellular organelle
GO:0043226	1.995e-02	79.95	97	2977	organelle
GO:0005930	2.006e-02	0.4834	4 DNAH8, DNAI2, EFHC1, TTC21B	18	axoneme
GO:0044428	2.106e-02	17.11	30	637	nuclear part
GO:0044430	2.336e-02	8.997	19	335	cytoskeletal part
GO:0031262	3.277e-02	0.08057	2 NUF2, SPC25	3	Ndc80 complex
GO:0000777	3.370e-02	0.94	5 CENPK, KIF2B, NEK2, NUF2, SPC25	35	condensed chromosome kinetochore
GO:0000779	3.370e-02	0.94	5 CENPK, KIF2B, NEK2, NUF2, SPC25	35	condensed chromosome, centromeric region
GO:0005815	4.392e-02	3.035	9	113	microtubule organizing center
GO:0031981	4.825e-02	13.54	24	504	nuclear lumen

HELP

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:0003777	1.852e-04	0.8325	8	30	microtubule motor activity
GO:0003676	5.341e-03	22.25	40	802	nucleic acid binding
GO:0003774	7.389e-03	1.526	8	55	motor activity
GO:0005488	1.053e-02	108.9	123	3924	binding

HELP

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.

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

HELP

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_m1_ca1	gga	ts	m	1
gga_ts_m2_ca1	gga	ts	m	2
mmu_ts_m1_ca1	mmu	ts	m	1
mmu_ts_m2_ca1	mmu	ts	m	2

Previous module | Next module Module #347, TG: 2.2, TC: 3, 194 probes, 191 Entrez genes, 4 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

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