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.

IEA

BP

GO:0000422

mitophagy

The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.

NAS

BP

GO:0001934

positive regulation of protein phosphorylation

Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.

IEA

BP

GO:0002376

immune system process

Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.

IEA

BP

GO:0006468

protein phosphorylation

The process of introducing a phosphate group on to a protein.

IEA

BP

GO:0006511

ubiquitin-dependent protein catabolic process

The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.

TAS

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.

IMP|TAS

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:0006950

response to 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 a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

TAS

BP

GO:0008104

protein localization

Any process in which a protein is transported to, or maintained in, a specific location.

TAS

BP

GO:0010821

regulation of mitochondrion organization

Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.

NAS

BP

GO:0016197

endosomal transport

The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.

TAS

BP

GO:0016236

macroautophagy

The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.

ISS|TAS

BP

GO:0016239

positive regulation of macroautophagy

Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.

IMP

BP

GO:0030154

cell differentiation

The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.

IEA

BP

GO:0035556

intracellular signal transduction

The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.

TAS

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.

TAS

BP

GO:0043066

negative regulation of apoptotic process

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

TAS

BP

GO:0043122

regulation of I-kappaB kinase/NF-kappaB signaling

Any process that modulates I-kappaB kinase/NF-kappaB signaling.

IMP

BP

GO:0044130

negative regulation of growth of symbiont in host

Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.

IEA

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.

TAS

BP

GO:0046578

regulation of Ras protein signal transduction

Any process that modulates the frequency, rate or extent of Ras protein signal transduction.

NAS

BP

GO:0051291

protein heterooligomerization

The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.

IEA

BP

GO:0061635

regulation of protein complex stability

Any process that affects the structure and integrity of a protein complex by altering the likelihood of its assembly or disassembly.

IDA

BP

GO:0098779

mitophagy in response to mitochondrial depolarization

The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.

IGI|TAS

CC

GO:0000407

pre-autophagosomal structure

A punctate structure localized in the vicinity of the vacuole that is required for the formation of autophagosomes.

IEA

CC

GO:0000932

cytoplasmic mRNA processing body

A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. mRNA processing and binding proteins are localized to these foci.

IDA

CC

GO:0005654

nucleoplasm

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

TAS

CC

GO:0005737

cytoplasm

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

IDA

CC

GO:0005770

late endosome

A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.

IEA

CC

GO:0005776

autophagosome

A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.

IDA

CC

GO:0005783

endoplasmic reticulum

The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

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:0016234

inclusion body

A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers.

IDA

CC

GO:0016235

aggresome

An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.

IBA

CC

GO:0016605

PML body

A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.

IDA

CC

GO:0031410

cytoplasmic vesicle

A vesicle found in the cytoplasm of a cell.

IEA

CC

GO:0044753

amphisome

An autophagosome formed upon fusion between autophagosomes and endosomes.

IDA

CC

GO:0044754

autolysosome

A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases.

IDA

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

CC

GO:0097225

sperm midpiece

The highly organized segment of the sperm flagellum which begins at the connecting piece and is characterized by the presence of 9 outer dense fibers (ODFs) that lie outside each of the 9 outer axonemal microtubule doublets and by a sheath of mitochondria that encloses the ODFs and the axoneme; the midpiece terminates about one-fourth of the way down the sperm flagellum at the annulus, which marks the beginning of the principal piece.

IEA

MF

GO:0004674

protein serine/threonine kinase activity

Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.

NAS

MF

GO:0005080

protein kinase C binding

Interacting selectively and non-covalently with protein kinase C.

IPI

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:0019901

protein kinase binding

Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.

IDA

MF

GO:0030971

receptor tyrosine kinase binding

Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.

TAS

MF

GO:0031625

ubiquitin protein ligase binding

Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.

IPI

MF

GO:0042169

SH2 domain binding

Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.

IDA

MF

GO:0042802

identical protein binding

Interacting selectively and non-covalently with an identical protein or proteins.

IPI

MF

GO:0042803

protein homodimerization activity

Interacting selectively and non-covalently with an identical protein to form a homodimer.

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.

IDA|TAS

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.

IEA