Module #66, TG: 4, TC: 1.4, 9 probes, 9 Entrez genes, 17 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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digestion

The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.

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.

multicellular organismal process

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

all

This term is the most general term possible

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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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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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calcium ion binding

Interacting selectively with calcium ions (Ca2+).

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.

serine-type endopeptidase activity

Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).

catalytic activity

Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

endopeptidase activity

Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.

serine-type peptidase activity

Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).

peptidase activity

Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.

binding

The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.

metal ion binding

Interacting selectively with any metal ion.

peptidase activity, acting on L-amino acid peptides

Catalysis of the hydrolysis of peptide bonds formed between L-amino acids.

hydrolase activity

Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

serine hydrolase activity

Catalysis of the hydrolysis of a substrate by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).

ion binding

Interacting selectively with ions, charged atoms or groups of atoms.

cation binding

Interacting selectively with cations, charged atoms or groups of atoms with a net positive charge.

all

This term is the most general term possible

calcium ion binding

Interacting selectively with calcium ions (Ca2+).

serine-type peptidase activity

serine-type endopeptidase activity

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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:0007586	2.764e-04	0.0259	3 PRSS1, PRSS2, PRSS3	27	digestion
GO:0032501	4.145e-02	1.581	6 NEFM, NRXN3, PRSS1, PRSS2, PRSS3, UGDH	1648	multicellular organismal process
GO:0006065	4.845e-02	0.0009594	1 UGDH	1	UDP-glucuronate biosynthetic process
GO:0031133	4.845e-02	0.0009594	1 NEFM	1	regulation of axon diameter
GO:0032536	4.845e-02	0.0009594	1 NEFM	1	regulation of cell projection size
GO:0046399	4.845e-02	0.0009594	1 UGDH	1	glucuronate biosynthetic 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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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.

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Id	Pvalue	ExpCount	Count	Size	Term
GO:0005509	1.553e-03	0.3639	5 NRXN3, PCDH9, PRSS1, PRSS2, PRSS3	402	calcium ion binding
GO:0004252	2.301e-03	0.04979	3 PRSS1, PRSS2, PRSS3	55	serine-type endopeptidase activity
GO:0008236	3.536e-03	0.05975	3 PRSS1, PRSS2, PRSS3	66	serine-type peptidase activity
GO:0017171	3.536e-03	0.05975	3 PRSS1, PRSS2, PRSS3	66	serine hydrolase activity
GO:0004175	3.388e-02	0.1639	3 PRSS1, PRSS2, PRSS3	181	endopeptidase 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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Id	Pvalue	ExpCount	Count	Size	Term
04080	3.262e-02	0.1827	3 PRSS1, PRSS2, PRSS3	83	Neuroactive ligand-receptor interaction

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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-TABM-263-raw-cel-1515485831.cel	10	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-3860-raw-cel-1561690360.cel	12	5	HGPS	hgu133a	none	GM0316B
E-GEOD-3860-raw-cel-1561690416.cel	15	5	HGPS	hgu133a	none	GM0316B
E-TABM-263-raw-cel-1515486191.cel	28	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-3860-raw-cel-1561690248.cel	5	5	HGPS	hgu133a	HGPS	AG11513
E-GEOD-3860-raw-cel-1561690472.cel	17	5	HGPS	hgu133a	none	GM00038C
E-TABM-263-raw-cel-1515486391.cel	38	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485671.cel	2	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486431.cel	40	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-3860-raw-cel-1561690199.cel	1	5	HGPS	hgu133a	none	GM0316B
E-TABM-263-raw-cel-1515485771.cel	7	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485811.cel	9	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515486371.cel	37	6	Cycle	hgu133a2	none	Cycle 1
E-TABM-263-raw-cel-1515485891.cel	13	6	Cycle	hgu133a2	none	Cycle 1
E-GEOD-3860-raw-cel-1561690432.cel	16	5	HGPS	hgu133a	HGPS	AG10750
E-GEOD-3860-raw-cel-1561690231.cel	4	5	HGPS	hgu133a	HGPS	AG10750
E-GEOD-3860-raw-cel-1561690336.cel	9	5	HGPS	hgu133a	HGPS	AG10750

Previous module | Next module Module #66, TG: 4, TC: 1.4, 9 probes, 9 Entrez genes, 17 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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