Module #122, TG: 2.4, TC: 1.6, 158 probes, 156 Entrez genes, 6 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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cell fate specification

The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.

multicellular organismal development

The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

nervous system development

The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.

central nervous system development

The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.

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.

glial cell differentiation

The process whereby a relatively unspecialized cell acquires the specialized features of a glial cell.

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.

spinal cord development

The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.

cell differentiation in spinal cord

The process whereby relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate.

spinal cord oligodendrocyte cell differentiation

The process whereby neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of oligodendrocytes. Oligodendrocytes are non-neuronal cells. The primary function of oligodendrocytes is the myelination of nerve axons in the central nervous system. Differentiation includes the processes involved in commitment of a cell to a specific fate.

spinal cord oligodendrocyte cell fate specification

The process whereby a cell becomes capable of differentiating autonomously into an oligodendrocyte in an environment that is neutral with respect to the developmental pathway.

oligodendrocyte cell fate specification

The process whereby a cell becomes capable of differentiating autonomously into an oligodendrocyte in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.

oligodendrocyte cell fate commitment

The process whereby the developmental fate of a cell becomes restricted such that it will develop into an oligodendrocyte.

glial cell fate specification

The process whereby a cell becomes capable of differentiating autonomously into a glial cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.

glial cell fate commitment

The process whereby the developmental fate of a cell becomes restricted such that it will develop into a glial cell.

neurogenesis

Generation of cells within the nervous system.

cell projection organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.

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.

neuron differentiation

The process whereby a relatively unspecialized cell acquires specialized features of a neuron.

regulation of cell projection organization

Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.

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.

gliogenesis

The process by which glial cells are generated. This includes the production of glial progenitors and their differentiation into mature glia.

cell fate commitment

The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.

generation of neurons

The process by which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons.

oligodendrocyte differentiation

The process whereby a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.

system development

The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.

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.

regulation of biological process

Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.

regulation of developmental process

Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

regulation of cellular process

Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

regulation of cellular component organization

Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

regulation of multicellular organismal process

Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.

regulation of nervous system development

Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.

biological regulation

Any process that modulates the frequency, rate or extent of any biological process, quality or function.

regulation of multicellular organismal development

Any process that modulates the frequency, rate or extent of multicellular organismal development.

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cell projection organization

multicellular organismal development

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.

regulation of developmental process

regulation of cellular process

regulation of cellular component organization

regulation of multicellular organismal process

regulation of biological process

regulation of cell projection organization

Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.

regulation of cell projection organization

Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.

regulation of multicellular organismal development

Any process that modulates the frequency, rate or extent of multicellular organismal development.

system development

regulation of multicellular organismal development

Any process that modulates the frequency, rate or extent of multicellular organismal development.

cell fate commitment

cell fate specification

The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.

cell differentiation in spinal cord

glial cell fate commitment

The process whereby the developmental fate of a cell becomes restricted such that it will develop into a glial cell.

glial cell fate specification

central nervous system development

neurogenesis

Generation of cells within the nervous system.

regulation of nervous system development

Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.

spinal cord development

oligodendrocyte differentiation

spinal cord oligodendrocyte cell differentiation

oligodendrocyte cell fate commitment

The process whereby the developmental fate of a cell becomes restricted such that it will develop into an oligodendrocyte.

spinal cord oligodendrocyte cell fate specification

The process whereby a cell becomes capable of differentiating autonomously into an oligodendrocyte in an environment that is neutral with respect to the developmental pathway.

glial cell differentiation

The process whereby a relatively unspecialized cell acquires the specialized features of a glial cell.

neuron differentiation

The process whereby a relatively unspecialized cell acquires specialized features of a neuron.

oligodendrocyte cell fate specification

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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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plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

membrane

Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.

integral to membrane

Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane.

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.

intrinsic to membrane

Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane.

membrane part

Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.

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.

membrane part

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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.

signal transducer activity

Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell.

receptor activity

Combining with an extracellular or intracellular messenger to initiate a change in cell activity.

transmembrane receptor activity

Combining with an extracellular or intracellular messenger to initiate a change in cell activity, and spanning to the membrane of either the cell or an organelle.

molecular transducer activity

The molecular function that accepts an input of one form and creates an output of a different form.

all

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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:0048709	6.550e-04	0.2972	5 C11orf9, NKX2-2, OLIG2, SOX10, SOX8	27	oligodendrocyte differentiation
GO:0022008	2.144e-03	5.624	17	511	neurogenesis
GO:0007399	2.818e-03	10.2	24	927	nervous system development
GO:0021515	4.788e-03	0.2531	4 CLN8, NKX2-2, OLIG2, PAX7	23	cell differentiation in spinal cord
GO:0021529	5.362e-03	0.02201	2 NKX2-2, OLIG2	2	spinal cord oligodendrocyte cell differentiation
GO:0021530	5.362e-03	0.02201	2 NKX2-2, OLIG2	2	spinal cord oligodendrocyte cell fate specification
GO:0031344	8.588e-03	1.222	7	111	regulation of cell projection organization
GO:0051960	9.643e-03	2.102	9	191	regulation of nervous system development
GO:0030182	9.803e-03	4.733	14	430	neuron differentiation
GO:0007422	1.018e-02	0.3192	4 SOX10, SOX8, TBCE, UGT8	29	peripheral nervous system development
GO:0050877	1.197e-02	7.991	19	726	neurological system process
GO:0021778	1.277e-02	0.03302	2 NKX2-2, OLIG2	3	oligodendrocyte cell fate specification
GO:0021779	1.277e-02	0.03302	2 NKX2-2, OLIG2	3	oligodendrocyte cell fate commitment
GO:0021780	1.277e-02	0.03302	2 NKX2-2, OLIG2	3	glial cell fate specification
GO:0060284	1.761e-02	2.333	9	212	regulation of cell development
GO:0010001	1.766e-02	0.6714	5 C11orf9, NKX2-2, OLIG2, SOX10, SOX8	61	glial cell differentiation
GO:0021510	1.825e-02	0.3852	4 CLN8, NKX2-2, OLIG2, PAX7	35	spinal cord development
GO:0007417	1.962e-02	3.984	12	362	central nervous system development
GO:0048699	2.130e-02	5.228	14	475	generation of neurons
GO:0048714	2.170e-02	0.04403	2 NKX2-2, OLIG2	4	positive regulation of oligodendrocyte differentiation
GO:0007409	2.284e-02	1.959	8	178	axonogenesis
GO:0007601	2.342e-02	1.97	8	179	visual perception
GO:0050953	2.342e-02	1.97	8	179	sensory perception of light stimulus
GO:0030030	2.452e-02	4.127	12	375	cell projection organization
GO:0045494	2.649e-02	0.1981	3 CDHR1, CLN8, CNGB1	18	photoreceptor cell maintenance
GO:0045664	2.740e-02	1.574	7	143	regulation of neuron differentiation
GO:0019226	2.754e-02	3.632	11	330	transmission of nerve impulse
GO:0015693	3.107e-02	0.05503	2 NIPA1, NIPAL4	5	magnesium ion transport
GO:0042063	3.193e-02	0.8035	5 C11orf9, NKX2-2, OLIG2, SOX10, SOX8	73	gliogenesis
GO:0023052	3.226e-02	30.78	46	2797	signaling
GO:0007010	3.305e-02	4.336	12	394	cytoskeleton organization
GO:0048667	3.376e-02	2.135	8	194	cell morphogenesis involved in neuron differentiation
GO:0000904	3.843e-02	2.719	9	247	cell morphogenesis involved in differentiation
GO:0048812	3.975e-02	2.212	8	201	neuron projection morphogenesis

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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:0031224	2.892e-06	43.23	73	3717	intrinsic to membrane
GO:0016021	6.797e-06	42.31	71	3638	integral to membrane
GO:0044425	1.763e-05	49.86	78	4287	membrane part
GO:0016020	2.075e-05	59.88	88	5148	membrane
GO:0005886	4.543e-04	30.52	52	2624	plasma membrane

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List of all enriched GO categories (molecular function), at the 0.05 p-value level.

The columns:

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

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

Clicking on the GO identifiers takes you to the Gene Ontology web pages.

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

Id	Pvalue	ExpCount	Count	Size	Term
GO:0004872	4.850e-05	10.88	29	992	receptor activity
GO:0004871	2.763e-04	14.74	33	1344	signal transducer activity
GO:0060089	2.763e-04	14.74	33	1344	molecular transducer activity
GO:0004888	7.311e-04	7.5	21	684	transmembrane receptor activity
GO:0005044	1.372e-02	0.3728	4 DMBT1, ENPP2, HHIPL1, TMPRSS5	34	scavenger receptor 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
hsa_br_m2_ca1	hsa	br	m	2
hsa_br_m1_ca1	hsa	br	m	1
hsa_br_f_ca1	hsa	br	f	_
hsa_br_m7_ca1	hsa	br	m	7
hsa_br_m3_ca1	hsa	br	m	3
hsa_br_m6_ca1	hsa	br	m	6

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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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