Module #24, TG: 4, TC: 2, 11 probes, 11 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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cell activation

A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.

immune system process

Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.

immune system development

The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, 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.

leukocyte differentiation

The process whereby a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a plasmacytoid dendritic cell or any cell of the myeloid leukocyte or lymphocyte lineages.

regulation of immune system process

Any process that modulates the frequency, rate, or extent of an immune system process.

negative regulation of immune system process

Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.

regulation of leukocyte activation

Any process that modulates the frequency, rate, or extent of leukocyte activation.

negative regulation of leukocyte activation

Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation.

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).

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.

hemopoiesis

The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.

lymphocyte differentiation

The process whereby a relatively unspecialized precursor cell acquires specialized features of B cells, T cells, or natural killer cells.

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.

B cell differentiation

The process whereby a precursor cell type acquires the specialized features of a B cell.

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.

B cell activation

The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.

leukocyte activation

A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.

regulation of B cell differentiation

Any process that modulates the frequency, rate or extent of B cell differentiation.

regulation of cell differentiation

Any process that modulates the frequency, rate or extent of cell differentiation, the process whereby relatively unspecialized cells acquire specialized structural and functional features.

regulation of lymphocyte differentiation

Any process that modulates the frequency, rate or extent of lymphocyte differentiation.

lymphocyte activation

A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.

organ development

Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.

negative regulation of biological process

Any process that stops, prevents or reduces 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.

negative regulation of cellular process

Any process that stops, prevents or reduces 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.

hemopoietic or lymphoid organ development

The process whose specific outcome is the progression of any organ involved in hemopoiesis or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation.

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 B cell activation

Any process that modulates the frequency, rate or extent of B cell activation.

regulation of cell activation

Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.

negative regulation of cell activation

Any process that stops, prevents or reduces the frequency, rate or extent of cell activation.

negative regulation of B cell activation

Any process that stops, prevents or reduces the frequency, rate or extent of B cell activation.

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 lymphocyte activation

Any process that modulates the frequency, rate or extent of lymphocyte activation.

negative regulation of lymphocyte activation

Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte activation.

biological regulation

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

all

This term is the most general term possible

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.

negative regulation of immune system process

Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.

negative regulation of cellular process

regulation of immune system process

Any process that modulates the frequency, rate, or extent of an immune system process.

negative regulation of biological process

regulation of developmental process

regulation of cellular process

regulation of multicellular organismal process

regulation of biological process

negative regulation of immune system process

Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.

regulation of leukocyte activation

Any process that modulates the frequency, rate, or extent of leukocyte activation.

negative regulation of leukocyte activation

Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation.

leukocyte activation

A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.

negative regulation of cell activation

Any process that stops, prevents or reduces the frequency, rate or extent of cell activation.

negative regulation of cellular process

regulation of cell activation

system development

regulation of cell differentiation

Any process that modulates the frequency, rate or extent of cell differentiation, the process whereby relatively unspecialized cells acquire specialized structural and functional features.

negative regulation of leukocyte activation

Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation.

regulation of lymphocyte activation

Any process that modulates the frequency, rate or extent of lymphocyte activation.

negative regulation of lymphocyte activation

Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte activation.

regulation of leukocyte activation

Any process that modulates the frequency, rate, or extent of leukocyte activation.

negative regulation of cell activation

Any process that stops, prevents or reduces the frequency, rate or extent of cell activation.

negative regulation of leukocyte activation

Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation.

regulation of cell differentiation

Any process that modulates the frequency, rate or extent of cell differentiation, the process whereby relatively unspecialized cells acquire specialized structural and functional features.

regulation of lymphocyte differentiation

Any process that modulates the frequency, rate or extent of lymphocyte differentiation.

immune system development

organ development

hemopoietic or lymphoid organ development

leukocyte differentiation

regulation of lymphocyte differentiation

Any process that modulates the frequency, rate or extent of lymphocyte differentiation.

negative regulation of lymphocyte activation

Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte activation.

regulation of lymphocyte differentiation

Any process that modulates the frequency, rate or extent of lymphocyte differentiation.

B cell differentiation

The process whereby a precursor cell type acquires the specialized features of a B cell.

regulation of B cell activation

Any process that modulates the frequency, rate or extent of B cell activation.

negative regulation of B cell activation

Any process that stops, prevents or reduces the frequency, rate or extent of B cell activation.

lymphocyte differentiation

The process whereby a relatively unspecialized precursor cell acquires specialized features of B cells, T cells, or natural killer cells.

regulation of B cell differentiation

Any process that modulates the frequency, rate or extent of B cell differentiation.

negative regulation of B cell activation

Any process that stops, prevents or reduces the frequency, rate or extent of B cell activation.

regulation of B cell differentiation

Any process that modulates the frequency, rate or extent of B cell differentiation.

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.

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.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0045577	1.816e-03	0.006168	2 CD24, INHBA	5	regulation of B cell differentiation
GO:0050869	5.276e-03	0.0111	2 CD24, INHBA	9	negative regulation of B cell activation
GO:0051250	1.357e-02	0.01974	2 CD24, INHBA	16	negative regulation of lymphocyte activation
GO:0002695	1.492e-02	0.02097	2 CD24, INHBA	17	negative regulation of leukocyte activation
GO:0050866	1.633e-02	0.0222	2 CD24, INHBA	18	negative regulation of cell activation
GO:0050864	1.922e-02	0.02467	2 CD24, INHBA	20	regulation of B cell activation
GO:0045619	2.075e-02	0.0259	2 CD24, INHBA	21	regulation of lymphocyte differentiation
GO:0002683	2.691e-02	0.03084	2 CD24, INHBA	25	negative regulation of immune system process
GO:0030183	3.153e-02	0.03454	2 CD24, INHBA	28	B cell differentiation

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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:0031225	2.635e-02	0.04919	2 CD24, NCAM1	39	anchored to membrane
GO:0043509	3.099e-02	0.001261	1 INHBA	1	activin A complex
GO:0048180	3.099e-02	0.001261	1 INHBA	1	activin complex
GO:0045211	3.682e-02	0.06054	2 GABRA5, PRR7	48	postsynaptic 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.

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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-GEOD-3860-raw-cel-1561690360.cel	12	5	HGPS	hgu133a	none	GM0316B
4319_WBS.CEL	5	8	WBS	hgu133plus2	WBS	WBS 1
E-GEOD-3860-raw-cel-1561690416.cel	15	5	HGPS	hgu133a	none	GM0316B
E-GEOD-3407-raw-cel-1437949721.cel	5	4	Cockayne	hgu133a	CS	CSB

Previous module | Next module Module #24, TG: 4, TC: 2, 11 probes, 11 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

Help | Hide | Top Help | Show | Top Conditions

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