Module #48, TG: 4, TC: 1.6, 8 probes, 8 Entrez genes, 7 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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chromosome organization

A process that is carried out at the cellular level that results in the formation, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information.

chromatin assembly or disassembly

The formation or destruction of chromatin structures.

nucleosome assembly

The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

DNA packaging

Any process by which DNA and associated proteins are formed into a compact, orderly structure.

establishment or maintenance of chromatin architecture

Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.

organelle organization

A process that is carried out at the cellular level which results in the formation, 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.

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.

cellular component organization

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

cellular component assembly

A cellular process that results in the assembly of a part of the cell.

chromatin assembly

The assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.

cellular macromolecular complex subunit organization

Any process carried out at the cellular level by which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex.

cellular macromolecular complex assembly

The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level.

nucleosome organization

A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of one or more nucleosomes.

macromolecular complex subunit organization

Any process by which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex.

macromolecular complex assembly

The aggregation, arrangement and bonding together of a set of macromolecules to form a complex.

protein-DNA complex assembly

The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex.

all

This term is the most general term possible

chromatin assembly

macromolecular complex assembly

The aggregation, arrangement and bonding together of a set of macromolecules to form a complex.

cellular macromolecular complex assembly

The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level.

chromatin assembly

nucleosome assembly

The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

nucleosome assembly

The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.

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.

chromatin

The ordered and organized complex of DNA and protein that forms the chromosome.

nucleosome

A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.

cellular_component

The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

cell

The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

chromosome

A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

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.

protein-DNA complex

A macromolecular complex containing both protein and DNA molecules.

organelle

Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

non-membrane-bounded organelle

Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.

intracellular organelle

Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.

intracellular non-membrane-bounded organelle

Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.

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.

intracellular organelle part

A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.

cell part

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

all

This term is the most general term possible

cell part

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

organelle part

intracellular non-membrane-bounded organelle

Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.

intracellular organelle part

intracellular part

intracellular organelle

intracellular organelle part

nucleosome

A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.

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.

nucleosome

A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.

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:0006334	5.460e-04	0.03335	3 H2BFS, HIST1H2BH, HIST1H2BK	40	nucleosome assembly
GO:0031497	6.602e-04	0.03585	3 H2BFS, HIST1H2BH, HIST1H2BK	43	chromatin assembly
GO:0034728	7.440e-04	0.03752	3 H2BFS, HIST1H2BH, HIST1H2BK	45	nucleosome organization
GO:0006323	1.658e-03	0.05086	3 H2BFS, HIST1H2BH, HIST1H2BK	61	DNA packaging
GO:0006333	2.610e-03	0.06087	3 H2BFS, HIST1H2BH, HIST1H2BK	73	chromatin assembly or disassembly
GO:0065004	7.452e-03	0.09339	3 H2BFS, HIST1H2BH, HIST1H2BK	112	protein-DNA complex assembly
GO:0042742	1.044e-02	0.01668	2 H2BFS, HIST1H2BK	20	defense response to bacterium
GO:0009617	2.962e-02	0.03335	2 H2BFS, HIST1H2BK	40	response to bacterium
GO:0006325	2.988e-02	0.1743	3 H2BFS, HIST1H2BH, HIST1H2BK	209	establishment or maintenance of chromatin architecture
GO:0015697	4.487e-02	0.0008338	1 SLC22A4	1	quaternary ammonium group transport

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

The columns:

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

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

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

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

Id	Pvalue	ExpCount	Count	Size	Term
GO:0000786	2.420e-05	0.01612	3 H2BFS, HIST1H2BH, HIST1H2BK	21	nucleosome
GO:0032993	6.635e-05	0.02304	3 H2BFS, HIST1H2BH, HIST1H2BK	30	protein-DNA complex
GO:0000785	1.215e-03	0.06757	3 H2BFS, HIST1H2BH, HIST1H2BK	88	chromatin
GO:0044427	9.827e-03	0.152	3 H2BFS, HIST1H2BH, HIST1H2BK	198	chromosomal part
GO:0005694	1.724e-02	0.1904	3 H2BFS, HIST1H2BH, HIST1H2BK	248	chromosome

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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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Id	Pvalue	ExpCount	Count	Size	Term
05322	3.924e-05	0.08036	4	54	Systemic lupus erythematosus

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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
2Twin.CEL	2	2	DS-twin	hgu133plus2	none	DS-twin 2
E-TABM-263-raw-cel-1515486411.cel	39	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-4219-raw-cel-1311956634.cel	19	7	Sph-mono	hgu133plus2	none	Sph-mon 1
E-TABM-263-raw-cel-1515485991.cel	18	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485731.cel	5	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486091.cel	23	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485751.cel	6	6	Cycle	hgu133a2	none	Cycle 1

Previous module | Next module Module #48, TG: 4, TC: 1.6, 8 probes, 8 Entrez genes, 7 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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