Table 4 Biological processes overrepresented in the modules

Blue

GO:0010564

regulation of cell cycle process

Any process that modulates 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.

GO:0000086

G2/M transition of mitotic cell cycle

Progression from G2 phase to M phase of the mitotic cell cycle. The molecular event responsible for this transition is the activation of the major cell cycle cyclin-dependent kinase (e.g. Cdc2 in S. pombe, CDC28 in S. cerevisiae, Cdk1 in human).

GO:0051325

interphase

A cell cycle process comprising the steps by which a cell progresses through interphase, the stage of cell cycle between successive rounds of chromosome segregation. Canonically, interphase is the stage of the cell cycle during which the biochemical and physiologic functions of the cell are performed and replication of chromatin occurs.

GO:0051329

interphase of mitotic cell cycle

Interphase occurring as part of the mitotic cell cycle. Canonically, interphase is the stage of the cell cycle during which the biochemical and physiologic functions of the cell are performed and replication of chromatin occurs. A mitotic cell cycle is one which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells.

GO:0007346

regulation of mitotic cell cycle

Any process that modulates the rate or extent of progress through the mitotic cell cycle.

GO:0000278

mitotic cell cycle

Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.

GO:0045184

establishment of protein localization

The directed movement of a protein to a specific location.

GO:0016482

cytoplasmic transport

The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, or within the cytoplasm of a cell.

Brown

GO:0006508

proteolysis

The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

GO:0030163

protein catabolic process

The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.

GO:0044257

cellular protein catabolic process

The chemical reactions and pathways resulting in the breakdown of a protein by individual cells.

GO:0044267

cellular protein metabolic process

The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.

GO:0042593

glucose homeostasis

Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.

GO:0019538

protein metabolic process

The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.

GO:0006325

chromatin organization

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

GO:0016568

chromatin modification

The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure.

Grey

GO:0017148

negative regulation of translation

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.

GO:0035264

multicellular organism growth

The increase in size or mass of an entire multicellular organism, as opposed to cell growth.

GO:0042035

regulation of cytokine biosynthetic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines.

GO:0042089

cytokine biosynthetic process

The chemical reactions and pathways resulting in the formation of cytokines, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.

GO:0042107

cytokine metabolic process

The chemical reactions and pathways involving cytokines, any of a group of proteins or glycoproteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.

GO:0006399

tRNA metabolic process

The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.

GO:0014065

phosphatidylinositol 3-kinase cascade

A series of reactions, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). PI3K cascades lie downstream of many cell surface receptor linked signaling pathways and regulate numerous cellular functions.

GO:0014066

regulation of phosphatidylinositol 3-kinase cascade

Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.

GO:0014068

positive regulation of phosphatidylinositol 3-kinase cascade

Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.

Turquoise

GO:0006366

transcription from RNA polymerase II promoter

The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).

GO:0000003

reproduction

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

GO:0045596

negative regulation of cell differentiation

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

GO:0006357

regulation of transcription from RNA polymerase II promoter

Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.

GO:0022414

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.

GO:0006979

response to oxidative stress

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

GO:0032990

cell part morphogenesis

The process in which the anatomical structures of a cell part are generated and organized.

GO:0006351

transcription, DNA dependent

The cellular synthesis of RNA on a template of DNA.

Yellow

GO:0045859

regulation of protein kinase activity

Any process that modulates the frequency, rate or extent of protein kinase activity.

GO:0043549

regulation of kinase activity

Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

GO:0043409

negative regulation of MAPK cascade

Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.

GO:0002764

immune response-regulating signaling pathway

The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to the activation, perpetuation, or inhibition of an immune response.

GO:0050865

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.

GO:0002682

regulation of immune system process

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

GO:0002684

positive regulation of immune system process

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

GO:0010741

negative regulation of intracellular protein kinase cascade

Any process that decreases the rate, frequency or extent of a series of reactions, mediated by protein kinases, which occurs as a result of a single trigger reaction or compound.

GO:0001932

regulation of protein phosphorylation

Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.

GO:0010627

regulation of intracellular protein kinase cascade

Any process that modulates the rate, frequency or extent of a series of reactions, mediated by protein kinases, which occurs as a result of a single trigger reaction or compound.