BP

GO:0000122

negative regulation of transcription from RNA polymerase II promoter

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

IMP

BP

GO:0001773

myeloid dendritic cell activation

The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.

ISS

BP

GO:0002218

activation of innate immune response

Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.

IDA

BP

GO:0002407

dendritic cell chemotaxis

The movement of a dendritic cell in response to an external stimulus.

ISS

BP

GO:0002437

inflammatory response to antigenic stimulus

An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.

IEP

BP

GO:0002643

regulation of tolerance induction

Any process that modulates the frequency, rate, or extent of tolerance induction.

IDA

BP

GO:0002840

regulation of T cell mediated immune response to tumor cell

Any process that modulates the frequency, rate, or extent of a T cell mediated immune response to tumor cell.

ISS

BP

GO:0006265

DNA topological change

The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.

ISS

BP

GO:0006309

apoptotic DNA fragmentation

The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.

TAS

BP

GO:0006310

DNA recombination

Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

ISS

BP

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.

IDA

BP

GO:0006914

autophagy

The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.

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.

IDA

BP

GO:0007204

positive regulation of cytosolic calcium ion concentration

Any process that increases the concentration of calcium ions in the cytosol.

IDA

BP

GO:0010506

regulation of autophagy

Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.

IMP

BP

GO:0017055

negative regulation of RNA polymerase II transcriptional preinitiation complex assembly

Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.

IDA

BP

GO:0031175

neuron projection development

The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).

ISS

BP

GO:0032072

regulation of restriction endodeoxyribonuclease activity

Any process that modulates the frequency, rate or extent of a restriction endodeoxyribonuclease activity, the catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks.

IDA

BP

GO:0032392

DNA geometric change

The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.

ISS

BP

GO:0032425

positive regulation of mismatch repair

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

IDA

BP

GO:0032689

negative regulation of interferon-gamma production

Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.

IDA

BP

GO:0032733

positive regulation of interleukin-10 production

Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.

IDA

BP

GO:0032735

positive regulation of interleukin-12 production

Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.

IMP

BP

GO:0033151

V(D)J recombination

The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).

IDA

BP

GO:0034165

positive regulation of toll-like receptor 9 signaling pathway

Any process that activates or increases the frequency, rate, or extent of toll-like receptor 9 signaling pathway.

ISS

BP

GO:0035711

T-helper 1 cell activation

The change in morphology and behavior of a T-helper 1 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.

IDA

BP

GO:0042104

positive regulation of activated T cell proliferation

Any process that activates or increases the rate or extent of activated T cell proliferation.

IMP

BP

GO:0043065

positive regulation of apoptotic process

Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.

IDA

BP

GO:0043277

apoptotic cell clearance

The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.

IDA

BP

GO:0043280

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.

IDA

BP

GO:0043371

negative regulation of CD4-positive, alpha-beta T cell differentiation

Any process that stops, prevents, or reduces the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation.

IDA

BP

GO:0043388

positive regulation of DNA binding

Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).

IDA

BP

GO:0043410

positive regulation of MAPK cascade

Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.

IDA

BP

GO:0043537

negative regulation of blood vessel endothelial cell migration

Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels.

IDA

BP

GO:0045063

T-helper 1 cell differentiation

The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma.

IMP

BP

GO:0045087

innate immune response

Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

TAS

BP

GO:0045944

positive regulation of transcription from RNA polymerase II promoter

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

IDA

BP

GO:0046330

positive regulation of JNK cascade

Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.

IDA

BP

GO:0050716

positive regulation of interleukin-1 secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 from a cell.

IDA

BP

GO:0050918

positive chemotaxis

The directed movement of a motile cell or organism towards a higher concentration of a chemical.

IEA

BP

GO:0051103

DNA ligation involved in DNA repair

The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.

ISS

BP

GO:0051106

positive regulation of DNA ligation

Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.

ISS

BP

GO:0070374

positive regulation of ERK1 and ERK2 cascade

Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.

IDA

BP

GO:0090026

positive regulation of monocyte chemotaxis

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

IDA

BP

GO:0097350

neutrophil clearance

The selective elimination of senescent neutrophils from the body by autoregulatory mechanisms.

IDA

BP

GO:1990774

tumor necrosis factor secretion

The regulated release of tumor necrosis factor from a cell. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.

IDA

BP

GO:2000778

positive regulation of interleukin-6 secretion

Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.

IDA

BP

GO:2001200

positive regulation of dendritic cell differentiation

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

IMP

CC

GO:0000793

condensed chromosome

A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.

IDA

CC

GO:0005576

extracellular region

The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

TAS

CC

GO:0005615

extracellular space

That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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:0005654

nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus.

TAS

CC

GO:0005768

endosome

A vacuole to which materials ingested by endocytosis are delivered.

IEA

CC

GO:0005793

endoplasmic reticulum-Golgi intermediate compartment

A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.

IEA

CC

GO:0005886

plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

IEA

CC

GO:0009986

cell surface

The external part of the cell wall and/or plasma membrane.

IDA

CC

GO:0017053

transcriptional repressor complex

A protein complex that possesses activity that prevents or downregulates transcription.

IDA

MF

GO:0000400

four-way junction DNA binding

Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.

ISS

MF

GO:0000405

bubble DNA binding

Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA.

ISS

MF

GO:0001530

lipopolysaccharide binding

Interacting selectively and non-covalently with lipopolysaccharide.

IDA

MF

GO:0001786

phosphatidylserine binding

Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.

IDA

MF

GO:0003684

damaged DNA binding

Interacting selectively and non-covalently with damaged DNA.

IDA|ISS

MF

GO:0003690

double-stranded DNA binding

Interacting selectively and non-covalently with double-stranded DNA.

ISS

MF

GO:0003697

single-stranded DNA binding

Interacting selectively and non-covalently with single-stranded DNA.

ISS

MF

GO:0003700

transcription factor activity, sequence-specific DNA binding

Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

IDA

MF

GO:0005125

cytokine activity

Functions to control the survival, growth, differentiation and effector function of tissues and cells.

ISS

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:0008134

transcription factor binding

Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.

IPI

MF

GO:0008301

DNA binding, bending

The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.

IMP|ISS

MF

GO:0016829

lyase activity

Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

IDA

MF

GO:0019958

C-X-C chemokine binding

Interacting selectively and non-covalently with a C-X-C chemokine; C-X-C chemokines have a single amino acid between the first two cysteines of the characteristic four cysteine motif.

IDA

MF

GO:0042056

chemoattractant activity

Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.

ISS

MF

GO:0044822

poly(A) RNA binding

Interacting non-covalently with a poly(A) RNA, a RNA molecule which has a tail of adenine bases.

IDA

MF

GO:0050786

RAGE receptor binding

Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.

ISS

MF

GO:0070182

DNA polymerase binding

Interacting selectively and non-covalently with a DNA polymerase.

IDA

MF

GO:0070491

repressing transcription factor binding

Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.

IPI

MF

GO:0097100

supercoiled DNA binding

Interacting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA.

ISS