Module #110, TG: 2.8, TC: 2.4, 24 probes, 23 Entrez genes, 11 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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reproduction

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

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.

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.

gamete generation

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

spermatogenesis

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

single fertilization

The union of male and female gametes to form a zygote.

binding of sperm to zona pellucida

The process by which the sperm binds to the zona pellucida glycoprotein layer of the egg. The process begins with the attachment of the sperm plasma membrane to the zona pellucida and includes attachment of the acrosome inner membrane to the zona pellucida after the acrosomal reaction takes place.

cell recognition

The process by which a cell in a multicellular organism interprets its surroundings.

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.

cell-cell recognition

Cell recognition between cells, usually involving the formation of specialized cell junctions.

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.

multicellular organismal process

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

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.

sperm-egg recognition

The initial contact step made between the sperm plasma membrane and outer layer of the egg during fertilization.

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.

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.

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reproductive process

reproductive cellular process

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

cell recognition

The process by which a cell in a multicellular organism interprets its surroundings.

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.

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.

gamete generation

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

sperm-egg recognition

The initial contact step made between the sperm plasma membrane and outer layer of the egg during fertilization.

sperm-egg recognition

The initial contact step made between the sperm plasma membrane and outer layer of the egg during fertilization.

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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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.

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.

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.

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.

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.

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.

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.

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 part

intracellular organelle

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.

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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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:0019953	2.802e-05	0.4596	7	145	sexual reproduction
GO:0007283	8.219e-04	0.2916	5 ADAD1, BOLL, HSF2BP, PIWIL1, SYCP1	92	spermatogenesis
GO:0048232	8.219e-04	0.2916	5 ADAD1, BOLL, HSF2BP, PIWIL1, SYCP1	92	male gamete generation
GO:0022414	1.153e-03	0.8906	7	281	reproductive process
GO:0000003	1.177e-03	0.8938	7	282	reproduction
GO:0007339	2.843e-03	0.009509	2 ZPBP, ZPBP2	3	binding of sperm to zona pellucida
GO:0009988	2.843e-03	0.009509	2 ZPBP, ZPBP2	3	cell-cell recognition
GO:0035036	2.843e-03	0.009509	2 ZPBP, ZPBP2	3	sperm-egg recognition
GO:0007276	3.152e-03	0.4089	5 ADAD1, BOLL, HSF2BP, PIWIL1, SYCP1	129	gamete generation
GO:0048610	5.508e-03	0.2345	4 ADAD1, PIWIL1, ZPBP, ZPBP2	74	reproductive cellular process
GO:0000279	5.927e-03	0.4818	5 BOLL, KIF11, PIWIL1, SYCP1, TTK	152	M phase
GO:0032504	9.622e-03	0.5483	5 ADAD1, BOLL, HSF2BP, PIWIL1, SYCP1	173	multicellular organism reproduction
GO:0048609	9.622e-03	0.5483	5 ADAD1, BOLL, HSF2BP, PIWIL1, SYCP1	173	reproductive process in a multicellular organism
GO:0022403	1.696e-02	0.6403	5 BOLL, KIF11, PIWIL1, SYCP1, TTK	202	cell cycle phase
GO:0007052	1.977e-02	0.02853	2 KIF11, TTK	9	mitotic spindle organization
GO:0007126	2.181e-02	0.149	3 BOLL, PIWIL1, SYCP1	47	meiosis
GO:0051321	2.181e-02	0.149	3 BOLL, PIWIL1, SYCP1	47	meiotic cell cycle
GO:0051327	2.181e-02	0.149	3 BOLL, PIWIL1, SYCP1	47	M phase of meiotic cell cycle
GO:0007049	2.884e-02	1.173	6 BOLL, DTL, KIF11, PIWIL1, SYCP1, TTK	370	cell cycle
GO:0007338	3.460e-02	0.0412	2 ZPBP, ZPBP2	13	single fertilization
GO:0022402	3.973e-02	0.8209	5 BOLL, KIF11, PIWIL1, SYCP1, TTK	259	cell cycle 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.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0043186	3.851e-03	0.01953	2 DDX4, PIWIL1	6	P granule
GO:0045495	3.851e-03	0.01953	2 DDX4, PIWIL1	6	pole plasm
GO:0060293	3.851e-03	0.01953	2 DDX4, PIWIL1	6	germ plasm
GO:0000801	4.546e-02	0.003255	1 SYCP1	1	central element
GO:0000802	4.546e-02	0.003255	1 SYCP1	1	transverse filament

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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.

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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
hsa_ts_m2_ca1	hsa	ts	m	2
oan_ts_m2_ca1	oan	ts	m	2
ggo_ts_m_ca1	ggo	ts	m	_
oan_ts_m1_ca1	oan	ts	m	1
oan_ts_m3_ca1	oan	ts	m	3
ppa_ts_m_ca1	ppa	ts	m	_
mml_ts_m1_ca1	mml	ts	m	1
mmu_ts_m1_ca1	mmu	ts	m	1
ptr_ts_m_ca1	ptr	ts	m	_
mml_ts_m2_ca1	mml	ts	m	2
mmu_ts_m2_ca1	mmu	ts	m	2

Previous module | Next module Module #110, TG: 2.8, TC: 2.4, 24 probes, 23 Entrez genes, 11 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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