BP

GO:0001922

B-1 B cell homeostasis

The process of regulating the proliferation and elimination of B cells of the B-1 subset such that the total number of B-1 B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity.

ISS

BP

GO:0002237

response to molecule of bacterial origin

Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.

IDA

BP

GO:0002634

regulation of germinal center formation

Any process that modulates the frequency, rate, or extent of germinal center formation.

ISS

BP

GO:0002677

negative regulation of chronic inflammatory response

Any process that stops, prevents, or reduces the frequency, rate, or extent of a chronic inflammatory response.

IEA

BP

GO:0006915

apoptotic process

A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.

IEA

BP

GO:0006954

inflammatory response

The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.

IEA

BP

GO:0010803

regulation of tumor necrosis factor-mediated signaling pathway

Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.

TAS

BP

GO:0016579

protein deubiquitination

The removal of one or more ubiquitin groups from a protein.

TAS

BP

GO:0031397

negative regulation of protein ubiquitination

Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.

IDA

BP

GO:0032088

negative regulation of NF-kappaB transcription factor activity

Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.

IDA

BP

GO:0032480

negative regulation of type I interferon production

Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.

TAS

BP

GO:0032495

response to muramyl dipeptide

Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.

IEA

BP

GO:0032691

negative regulation of interleukin-1 beta production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production.

IEA

BP

GO:0032703

negative regulation of interleukin-2 production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.

IMP

BP

GO:0032715

negative regulation of interleukin-6 production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.

ISS

BP

GO:0032720

negative regulation of tumor necrosis factor production

Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.

ISS

BP

GO:0034136

negative regulation of toll-like receptor 2 signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 2 signaling pathway.

NAS

BP

GO:0034140

negative regulation of toll-like receptor 3 signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 3 signaling pathway.

IDA

BP

GO:0034144

negative regulation of toll-like receptor 4 signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 4 signaling pathway.

NAS

BP

GO:0034148

negative regulation of toll-like receptor 5 signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 5 signaling pathway.

IEA

BP

GO:0035871

protein K11-linked deubiquitination

A protein deubiquitination process in which a K11-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers, is removed from a protein.

IDA

BP

GO:0043124

negative regulation of I-kappaB kinase/NF-kappaB signaling

Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.

IDA

BP

GO:0045732

positive regulation of protein catabolic process

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

IDA

BP

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.

IEA

BP

GO:0045779

negative regulation of bone resorption

Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.

NAS

BP

GO:0045824

negative regulation of innate immune response

Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.

ISS

BP

GO:0048662

negative regulation of smooth muscle cell proliferation

Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.

IDA

BP

GO:0050691

regulation of defense response to virus by host

Any host process that modulates the frequency, rate, or extent of the antiviral response of a host cell or organism.

NAS

BP

GO:0050727

regulation of inflammatory response

Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.

IBA

BP

GO:0050728

negative regulation of inflammatory response

Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.

ISS

BP

GO:0050869

negative regulation of B cell activation

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

ISS

BP

GO:0051259

protein oligomerization

The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.

NAS

BP

GO:0061043

regulation of vascular wound healing

Any process that modulates the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature.

NAS

BP

GO:0070301

cellular response to hydrogen peroxide

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.

ISS

BP

GO:0070423

nucleotide-binding oligomerization domain containing signaling pathway

Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein.

TAS

BP

GO:0070429

negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 1 (NOD1) pathway.

IEA

BP

GO:0070433

negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) pathway.

IEA

BP

GO:0070536

protein K63-linked deubiquitination

A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.

IDA

BP

GO:0070936

protein K48-linked ubiquitination

A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.

IDA

BP

GO:0071108

protein K48-linked deubiquitination

A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.

IDA

BP

GO:0071222

cellular response to lipopolysaccharide

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.

IDA

BP

GO:0071947

protein deubiquitination involved in ubiquitin-dependent protein catabolic process

The removal of one or more ubiquitin groups from a protein as part of a process of ubiquitin-dependent protein catabolism.

IBA

BP

GO:0072573

tolerance induction to lipopolysaccharide

Tolerance induction directed at lipopolysaccharide antigens.

IMP

BP

GO:0072666

establishment of protein localization to vacuole

The directed movement of a protein to a specific location in a vacuole.

IEA

BP

GO:0090291

negative regulation of osteoclast proliferation

Any process that decreases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population.

NAS

BP

GO:1902042

negative regulation of extrinsic apoptotic signaling pathway via death domain receptors

Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.

IDA

BP

GO:1903364

positive regulation of cellular protein catabolic process

Any process that activates or increases the frequency, rate or extent of cellular protein catabolic process.

IEA

BP

GO:2000347

positive regulation of hepatocyte proliferation

Any process that activates or increases the frequency, rate or extent of hepatocyte proliferation.

IEA

BP

GO:2000349

negative regulation of CD40 signaling pathway

Any process that stops, prevents or reduces the frequency, rate or extent of signaling via the CD40 signaling pathway.

IMP

BP

GO:2000352

negative regulation of endothelial cell apoptotic process

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

IDA

CC

GO:0005634

nucleus

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

IDA

CC

GO:0005737

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

IBA

CC

GO:0005764

lysosome

A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

IEA

CC

GO:0005829

cytosol

The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

TAS

CC

GO:0070062

extracellular exosome

A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

IDA

MF

GO:0002020

protease binding

Interacting selectively and non-covalently with any protease or peptidase.

IPI

MF

GO:0003677

DNA binding

Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

IEA

MF

GO:0004842

ubiquitin-protein transferase activity

Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.

IDA

MF

GO:0004843

thiol-dependent ubiquitin-specific protease activity

Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.

IDA|TAS

MF

GO:0005515

protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

IPI

MF

GO:0008270

zinc ion binding

Interacting selectively and non-covalently with zinc (Zn) ions.

IEA

MF

GO:0016874

ligase activity

Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.

IEA

MF

GO:0019900

kinase binding

Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.

IEA

MF

GO:0043130

ubiquitin binding

Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.

IPI

MF

GO:0043621

protein self-association

Interacting selectively and non-covalently with a domain within the same polypeptide.

IDA

MF

GO:0070530

K63-linked polyubiquitin binding

Interacting selectively and non-covalently and non-covalently with a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers.

IBA