GO:0006751

BP

glutathione catabolic process

The chemical reactions and pathways resulting in the breakdown of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.

CHAC2, CHAC1

GO:0006754

BP

ATP biosynthetic process

The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

ATP5H, ATP5L, TGFB1, ALDOA, ATP5J, ATP5D, ATP5C1, ATP5O, ATP5G3, ATP5E, ATP5I, ATP5G2, UQCC3, CHCHD10, SLC25A13

GO:0006760

BP

folic acid-containing compound metabolic process

The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.

MTHFD1L

GO:0006766

BP

vitamin metabolic process

The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.

CYP27B1, CYP26A1, CYP2R1, CYP26B1

GO:0006768

BP

biotin metabolic process

The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.

ACACB, VNN1, PCCA, PC, PDZD11, MCCC1, MCCC2, VNN3

GO:0006769

BP

nicotinamide metabolic process

The chemical reactions and pathways involving nicotinamide, pyridine-3-carboxamide, the amide of nicotinic acid. It is a member of the B complex of vitamins and occurs widely in living organisms.

PTGS2, NAMPT, PTGIS, CARKD

GO:0006771

BP

riboflavin metabolic process

The chemical reactions and pathways involving riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

ENPP1, RFK, SLC52A3

GO:0006772

BP

thiamine metabolic process

The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

ACPP, TPK1

GO:0006776

BP

vitamin A metabolic process

The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene.

ALDH1A2, RBP1, PPARD

GO:0006777

BP

Mo-molybdopterin cofactor biosynthetic process

The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.

MOCOS, GPHN

GO:0006778

BP

porphyrin-containing compound metabolic process

The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

CYP1A1

GO:0006779

BP

porphyrin-containing compound biosynthetic process

The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

ABCB6

GO:0006781

BP

succinyl-CoA pathway

The chemical reactions that utilize succinyl-CoA in the synthesis of protoporphyrin IX.

SUCLA2

GO:0006782

BP

protoporphyrinogen IX biosynthetic process

The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

UROD, ALAD, CPOX

GO:0006783

BP

heme biosynthetic process

The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.

UROD, ALAD, TSPO, CPOX, SLC11A2, NFE2L1, FXN, IBA57, SLC25A39, TMEM14C

GO:0006788

BP

heme oxidation

The chemical reactions and pathways resulting in the loss of electrons from one or more atoms in heme.

HMOX1

GO:0006790

BP

sulfur compound metabolic process

The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.

PAX8, CHST3, CHST4, ISCA1, CHST5, CHST6, CHST7, CHST2

GO:0006796

BP

phosphate-containing compound metabolic process

The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.

ENPP3, TGFB1, ACYP1, ENPP1, PTPRB, PTPRD, IMPA1, INPP1, ENPP2, SLC20A1, INPP5D

GO:0006797

BP

polyphosphate metabolic process

The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.

MINPP1

GO:0006801

BP

superoxide metabolic process

The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

SH3PXD2B, CCS, SOD2, CYBB, NCF2, NOXA1, NOX4

GO:0006805

BP

xenobiotic metabolic process

The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.

AIP, MGST3, GSTA4, CYP26A1, AKR7A2, AOC2, CYP2E1, UGT2B4, EPHX1, CYP3A4, GSTP1, SULT1A3, MGST1, CYP2D6, CYP2C9, NQO1, CYP2B6, CYP3A5, AADAC, PTGS1, CYP3A7, RORA, AHR, AKR1C1, CYP1B1, AOC3, CYP2W1, FMO2, MGST2, GSTO2, CYP26B1

GO:0006807

BP

nitrogen compound metabolic process

The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium.

VNN1, PKD1, MYO1E, VNN3, SEC63

GO:0006808

BP

regulation of nitrogen utilization

Any process that modulates the frequency, rate or extent of nitrogen utilization.

BCL2, BAX

GO:0006809

BP

nitric oxide biosynthetic process

The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.

DDAH2, NQO1, NOS3, AKT1, RORA, SLC7A2, CYP1B1

GO:0006810

BP

transport

The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

FABP12, SLC33A1, GOLIM4, ABCC5, AQP9, ASNA1, ENSA, SLC37A4, MPDU1, SEC14L2, AQP8, ABCA8, SLC25A14, PMP2, TTR, ALB, SLC25A5, DBI, GNAI3, RBP1, PAEP, AR, SLC25A4, CFTR, FABP4, SLC25A16, GJA1, ATP2B1, CNGA1, SLC6A1, CHRNA5, SRI, SLC6A6, GABRA5, ABCC1, GJC1, PTGDS, CRAT, SLC6A8, GRIA4, CLCN3, CLCN4, CLCN5, CLCN7, CLCNKA, CLCNKB, SLC7A2, CACNB3, OAZ1, ATP1B3, SLC12A2, UCP2, SMAD3, PITPNA, SLC25A3, SLC7A5, SLC20A2, CDH17, GRIN2A, G3BP1, TCOF1, LAPTM5, ITPR2, CLCA4, PEA15, RALBP1, CACNA1E, SLC15A2, LDLRAP1, ACBD5, SYPL2, CHIC1, SLC27A4, SLC51A, LAPTM4B, CREBRF, SLC35F2, TRPV1, SLC20A1, AQP3, SLC7A6, SLC9A6, SLC5A5, P2RX4, FEZ1, TM9SF2, TTPAL, SLC25A39, ACBD3, ABCB6, ABCB10, STAU2, CLIC5, TMEM9, ABCF2, ASIC3, SLC7A8, SLC25A13, SLC7A7, SLC6A14, TCAF1, MYO5A, TRPV2, LYVE1, SLC4A4

GO:0006811

BP

ion transport

The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

GPR89A, TMEM63A, TOMM40, CYBB, GPR89B, CHRNA7, SLC1A3, SLC1A2, GLRB, SLC1A6, SLC26A2, SLC12A2, LCN2, SLC20A2, SLC15A2, FXN, SLC25A26, SLC36A1, TMC6, SLC15A4, SLC20A1, SLC9A6, SLC5A5, PANX2, SLC26A1, WNK1, SLC24A3, SLC25A10, SLC9A2, ATP11B

GO:0006812

BP

cation transport

The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

CHRNB1, ANO6, PIEZO1, PANX1, TRPC6

GO:0006813

BP

potassium ion transport

The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

KCNK1, KCNK3, VPS4B, CDK2, GJA5, NSF, CDKN1B, ATP1A2, SLC12A2, KCNA1, KCNMA1, KCNJ12, KCNK17, CHP1, SLC24A3, KCNIP2, KCNG1, KCNK6

GO:0006814

BP

sodium ion transport

The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC22A5, TRAPPC10, ATP1A2, SCNN1G, SLC12A2, SLC10A7, SCN9A, SLC4A8, MFSD4B, SLC5A11, NEDD4L, SLC38A1, SLC38A10, SLC4A4

GO:0006816

BP

calcium ion transport

The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

CYP27B1, RAMP1, RAMP3, PRKCB, FYN, ANXA6, SLC3A2, CCL3, VDR, CCL5, TPT1, PLN, SRI, CORO1A, CHRNA7, TRPC1, PSEN2, CACNB3, CACNA2D1, CCL8, ATP2C1, CAV1, PPP3CA, TRPC3, CAMK2D, PKD2, ITPR1, RYR3, CACHD1, BSPRY, CACNG8, RYR2, PANX1, CACNG6, TRPV6, TRPV4

GO:0006817

BP

phosphate ion transport

The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

IP6K2

GO:0006820

BP

anion transport

The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC4A2, TSPO, VDAC2, LRRC8A, VDAC3

GO:0006821

BP

chloride transport

The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

FXYD1, CLIC1, BEST1, CLIC3, TSPO, CLCN4, CLCN6, ANO6, SLC26A1, TTYH1, CLIC5

GO:0006824

BP

cobalt ion transport

The directed movement of cobalt (Co) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC11A2

GO:0006825

BP

copper ion transport

The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

ATOX1, SLC31A1, SLC31A2, SLC11A2, FKBP4, COX17, HEPH

GO:0006826

BP

iron ion transport

The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

FTL, FTH1, SLC11A1, NECTIN1, HEPH, TTYH1, SFXN1, TFR2

GO:0006828

BP

manganese ion transport

The directed movement of manganese (Mn) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

ZP3, TRPC1, SLC11A1, SLC11A2, TRPC3, TRPC6

GO:0006829

BP

zinc II ion transport

The directed movement of zinc (Zn II) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

MT3, SLC30A9, SLC30A8, SLC39A8, SLC30A1

GO:0006833

BP

water transport

The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

AQP9, AQP8, MIP, AQP2, SLC14A1, AQP3

GO:0006835

BP

dicarboxylic acid transport

The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC25A10

GO:0006836

BP

neurotransmitter transport

The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.

SLC22A1, SYNJ1, SLC6A1, SLC6A6, SLC6A8, ICA1, SLC6A14

GO:0006837

BP

serotonin transport

The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems.

SLC18A2

GO:0006839

BP

mitochondrial transport

Transport of substances into, out of or within a mitochondrion.

SLC25A14, HSP90AA1, UCP1, PSEN1, UCP2, UCP3, STARD3, SLC25A30, SLC25A10

GO:0006851

BP

mitochondrial calcium ion transport

The directed movement of calcium ions (Ca2+) into, out of or within a mitochondrion.

MICU2, MCUR1, SLC25A23

GO:0006853

BP

carnitine shuttle

The transfer of acyl groups to and from acyl-CoA molecules to form O-acylcarnitine, which can exchange across the mitochondrial inner membrane with unacylated carnitine.

ACACB, CPT1A, PRKAA2, CPT1B

GO:0006855

BP

drug transmembrane transport

The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.

SLC22A1, SLC31A1, ATP8B1, SLC22A3, SLC22A5, ABCA8, EBP, SLC22A18, SLC47A1, TMEM30A

GO:0006857

BP

oligopeptide transport

The directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.

CDH17, SLC15A2, SLC15A4

GO:0006860

BP

extracellular amino acid transport

The directed extracellular movement of amino acids.

SLC1A5

GO:0006863

BP

purine nucleobase transport

The directed movement of purine bases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

AQP9

GO:0006864

BP

pyrimidine nucleotide transport

The directed movement of a pyrimidine nucleotide, any compound consisting of a pyrimidine nucleoside esterified with (ortho)phosphate, into, out of or within a cell.

SLC25A36

GO:0006865

BP

amino acid transport

The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC3A2, SLC6A6, SLC1A4, SLC7A2, SLC7A9, SLC7A5, SLC1A5, SLC36A1, SLC16A10, SLC38A5, SLC7A6, SLC38A1, SLC7A8, SLC7A7, SLC6A14, SLC7A11

GO:0006867

BP

asparagine transport

The directed movement of asparagine, alpha-aminosuccinamic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC38A1

GO:0006868

BP

glutamine transport

The directed movement of glutamine, 2-amino-4-carbamoylbutanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

SLC1A4, SLC1A5, SLC38A1

GO:0006869

BP

lipid transport

The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.

ESYT2, NME4, ABCA8, APOD, SERPINA5, PSAP, GM2A, TSPO, CHKA, VLDLR, HDLBP, APOBR, STARD3, ANO6, APOA5, LRP10, ABCA6, ABCA5, SORL1, SLCO2A1, APOLD1, OSBPL9, SIGMAR1, APOL2, ESYT1, APOO, OSBPL11, OSBPL10, OSBPL1A, OSBPL6, PCTP

GO:0006874

BP

cellular calcium ion homeostasis

Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.

STC2, VAPB, TGFB1, PTH, APOE, ATP1B1, PRKCB, CCL3, VDR, CCL2, CCL5, TPT1, TNNI3, ATP2B1, ATP2B4, CALR, HTR2C, CHRNA7, HTR2B, PIK3CB, CXCL12, STC1, CCL8, ATP2C1, ANK2, CAV1, DMPK, RGN, ATP13A5, SYPL2, SV2A, CHERP, TPCN2, RYR2, TMEM203, ATP13A3, TRPV4, TMEM165, SLC24A3, ATP13A2, STIM2, SLC30A1

GO:0006875

BP

cellular metal ion homeostasis

Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell.

LETM1, MT3, LETM2

GO:0006876

BP

cellular cadmium ion homeostasis

Any process involved in the maintenance of an internal steady state of cadmium ions at the level of a cell.

SLC11A1

GO:0006878

BP

cellular copper ion homeostasis

Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.

ATOX1, SLC31A1, SLC31A2, MT2A, PRNP, APP, ARF1, PRND

GO:0006879

BP

cellular iron ion homeostasis

Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.

MYC, TFRC, TF, FTL, FTH1, HMOX1, BMP6, SLC11A1, SLC11A2, LCN2, HAMP, SMAD4, FXN, HIF1A, HFE, CYBRD1, TMPRSS6, SLC46A1, HEPH, NDFIP1, ABCB6, SLC40A1, ATP13A2, TFR2

GO:0006880

BP

intracellular sequestering of iron ion

The process of binding or confining iron ions in an intracellular area such that they are separated from other components of a biological system.

FTL, FTH1, SRI

GO:0006882

BP

cellular zinc ion homeostasis

Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.

MT3, MT1X, SLC39A6, SLC39A14, SLC39A4, SLC30A8, SLC39A8, ATP13A2, SLC39A10, SLC30A1

GO:0006883

BP

cellular sodium ion homeostasis

Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell.

AGT, ATP1B1, AGTR2, ATP1A2, ATP12A, ATP1B3, SGK3, NEDD4L

GO:0006884

BP

cell volume homeostasis

Any process involved in maintaining the steady state of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell.

CLCN6, LRRC8A, TRPV4

GO:0006885

BP

regulation of pH

Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.

EDN1, CLCN3, ATP12A, PDK4

GO:0006886

BP

intracellular protein transport

The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.

AP3D1, DSCR3, STX7, STX6, TBC1D4, TBC1D12, RAMP1, RAMP3, PDCD6, VPS26A, STX11, AP1G2, STAM2, SEC24D, AP2A2, SNAPIN, TBC1D8, CD74, SCG5, NPM1, NGFR, CLTA, TBC1D3H, ZP3, KDELR1, CHML, ERP29, STX2, NSF, ARCN1, TMED10, BCAP31, ARFIP1, COPA, AP3M2, AP2S1, SEC13, AP1S2, AP3S2, COPZ1, AP1S1, RHOB, AP2B1, CDK5, APBA1, YWHAH, TBC1D8B, AP1B1, STX4, STX3, SNX1, CTTN, TMED2, SEC23A, RABGAP1L, WLS, GRTP1, TBC1D9B, TBC1D3C, TBC1D9, HID1, TBC1D3, EXPH5, MYRIP, TBC1D16, TBC1D15, SYTL5, SNX33, TBC1D5, APPBP2, USP6NL, STAM, RPGR, ARHGEF2, ACD, SYTL4, RUNDC1, EVI5L, AP2M1, VPS35, SNX18, MLPH, IFT27, ASPSCR1, NAPB, RAB3GAP2, SYTL2, ARFGAP3, SNX15, TBC1D14, HDAC6, VPS29, GGA2, GGA1, TLK1, ANKRD50, MYO6, SYNRG, RPH3AL, SNX6, TBC1D2B, RIMS2, RABGAP1, SNX9, SNX5, COPG1, SAR1B

GO:0006887

BP

exocytosis

A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This process begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when vesicle fusion is complete. This is the process in which most molecules are secreted from eukaryotic cells.

WASH1, MYO1G, PIK3C2A, EXOC5, SCAMP1, EXOC3, VAMP4, SNAP29, CCL3, RALA, CCL5, NSF, RAB27A, PRSS12, VAMP2, CCL8, CDK16, TNFAIP2, VAMP3, PDZD11, STXBP5, SNX19, VMP1, LIN7B, SYTL2, LIN7C, EXOC1, RPH3AL, EXOC7, STXBP5L, MYO5A, ARFGEF2

GO:0006888

BP

ER to Golgi vesicle-mediated transport

The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.

DCTN6, DYNC1I1, COPE, GOSR2, DYNC1LI2, SEC22B, SEC24D, SEC31A, VAPB, F8, F2, SERPINA1, TGFA, INS, BGLAP, CD55, TRAPPC2, F5, FOLR1, AREG, ARF4, KDELR1, NSF, ARCN1, TMED10, BCAP31, VAMP7, COPA, CTSC, VCP, COPZ1, RAB1A, DYNLL1, SPTBN1, ANK2, GOLGA2, ANK3, DYNC1I2, DCTN2, CUL3, DCTN1, DYNC1H1, GAS6, COG2, TMED2, SEC23A, KLHL12, TEX261, ARFGAP2, MCFD2, DYNC2LI1, GBF1, ERGIC1, SEC22A, LMF1, DCTN5, RAB1B, LMAN2L, SPTBN4, GOPC, RANGRF, ARFGAP3, NRBP2, BET1L, VAPA, SPAST, CTSZ, VTI1B, COG6, TMED3, HYOU1, TRAPPC1, IER3IP1, COPG1, SAR1B

GO:0006890

BP

retrograde vesicle-mediated transport, Golgi to ER

The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.

COPE, SURF4, KDELR3, KIF1C, ATP9A, SEC22B, KIF4A, ARF4, KDELR1, HTT, NSF, ARCN1, PITPNB, TMED10, KIF11, COPA, COPZ1, RAB1A, ARF5, CENPE, KIF23, KIF22, TMED2, ARFGAP2, KIF18A, GBF1, KIFAP3, SCYL1, ERGIC2, KIF2C, RACGAP1, RAB1B, ARFGAP3, RAB6B, KIF15, TMED3, KIF3A, COPG1

GO:0006891

BP

intra-Golgi vesicle-mediated transport

The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).

COPE, GOSR2, NSF, TRAPPC10, COPA, GABARAPL2, COPZ1, COG2, RAB6B, VTI1B, COG6

GO:0006892

BP

post-Golgi vesicle-mediated transport

The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles.

SNAP23, EXOC5, SCAMP1, SCAMP2, RP2, VAMP7, VAMP2, ARF1, STX4, GBF1, SORL1, MYO5A

GO:0006893

BP

Golgi to plasma membrane transport

The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.

CCDC93, COMMD1, STXBP6, EXOC2, GOPC, EXOC1, ARFGEF2

GO:0006895

BP

Golgi to endosome transport

The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes.

RAB29, EPS15, VPS13C, MON2, GBF1

GO:0006896

BP

Golgi to vacuole transport

The directed movement of substances from the Golgi to the vacuole.

GOSR2, VTI1B

GO:0006897

BP

endocytosis

A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.

ESYT2, WIPF3, PIK3C2A, BIN1, NPC1, LY75, ATP9A, LRP5, SNX4, LDLR, APP, GHR, NME1, RAB5A, CHRNA7, CSNK1D, PIK3CG, CSNK1E, TSC2, RAB7A, VAMP7, RAB1A, LRP2, TNK2, MYO1E, UNC119, EEA1, RABEP1, RALBP1, TRIP10, DPYSL2, AAK1, ARC, MIB1, NOSTRIN, DNER, RIN3, DENND1A, SNX33, STAB2, RIN2, HOOK2, C9orf72, SNX18, FNBP1, SIGLEC1, CSNK1G1, CD209, ITSN2, SH3BP4, ANKFY1, ATP6V1H, RABGEF1, RAB22A, MYO6, SYNRG, SNX6, USP20, SNX9, CSNK1G3, STON1

GO:0006898

BP

receptor-mediated endocytosis

An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.

ENPP3, CD5L, HP, LDLR, APOA1, APOE, AMBP, ALB, VTN, APOB, CFI, ADRB2, HSP90AA1, CD14, SPARC, SAA1, IGF2R, FCGR1A, HSP90B1, FOLR1, CD36, ENPP1, MRC1, CALR, CD6, LRPAP1, TGFBR2, PPT1, PRSS12, AP1S1, HBB, HBA1, OLR1, DAB2, VLDLR, LRP2, APOBR, CLN3, PICALM, ENPP2, SCARF1, CTTN, COLEC12, LDLRAP1, LRP10, RABEPK, CD163, SBSPON, SCARB1, STAB2, HSPH1, FCGR1B, SORL1, PRG4, LOXL4, TINAGL1, CXCL16, ACKR4, PDLIM7, CD163L1, STAB1, PI4KB, DMBT1, TFR2, LOXL2, HYOU1, SNX9

GO:0006900

BP

membrane budding

The evagination of a membrane, resulting in formation of a vesicle.

WASL, ANXA2, S100A10, FNBP1L

GO:0006903

BP

vesicle targeting

The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo.

SNAP23, SNAP29, LRMP

GO:0006904

BP

vesicle docking involved in exocytosis

The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.

CFTR, STXBP1, STXBP2, VAMP3, CPLX2, RABEPK, SCFD2, RAB8B, EXOC4, SYTL2, VTI1B

GO:0006906

BP

vesicle fusion

Fusion of the membrane of a transport vesicle with its target membrane.

STX7, STX6, GNAI3, SYT1, CAV2, VAMP7, VAMP2, LRMP, EEA1, VAMP3, C2CD5, SYTL5, SYTL4, SYT11, SYTL2, VAV3, RPH3AL

GO:0006907

BP

pinocytosis

An endocytosis process that results in the uptake of liquid material by cells from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, called pinosomes, formed by invagination of the plasma membrane.

AHSG, PPT1, EHD4, SNX5

GO:0006909

BP

phagocytosis

An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.

CDC7, PIP5K1C, CEACAM4, TUSC2, ANXA1, ITGB2, CD14, ANXA3, PECAM1, RAB5A, ADORA1, CORO1A, LEP, LEPR, CSNK1A1, SLC11A1, ANXA11, MERTK, GAS6, CD302, CD93, CDC42SE2, CDC42SE1, CORO1C

GO:0006910

BP

phagocytosis, recognition

The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.

IGLL5, CD36, MFGE8, COLEC12, CLEC7A

GO:0006911

BP

phagocytosis, engulfment

The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.

IGLL5, ABCA1, FCGR1A, MYH9, VAMP7, MFGE8, ELMO1, BIN2

GO:0006913

BP

nucleocytoplasmic transport

The directed movement of molecules between the nucleus and the cytoplasm.

NPM1, ANP32A, EIF5A, CDK5, SET, CAMK1, FBXO22, NUP205, RSRC1, CITED1, MYBBP1A, ANP32E, UPF3A

GO:0006914

BP

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.

VPS37C, TECPR2, NPC1, CHMP2A, VPS4B, STAM2, S100A8, S100A9, CTSD, HMGB1, LAMP1, ARSB, ITGB4, XBP1, TFEB, PIK3CB, DAP, VCP, SESN2, GABARAPL2, RAB1A, FOXO1, SQSTM1, STK11, IFI16, WIPI1, FNBP1L, RAB12, DRAM2, TECPR1, SIRT2, DRAM1, PIK3C3, VPS37A, RB1CC1, TBC1D5, STAM, USP13, MVB12A, NRBF2, VMP1, C9orf72, TMEM59, TOLLIP, RAB1B, ATG10, CHMP4B, VTA1, UBQLN4, PTPN22, SH3GLB1, WDR45

GO:0006915

BP

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.

APBB1, HIP1, EBAG9, MAP2K7, PDCD5, PLSCR1, AXIN1, OGT, BIRC5, TOX3, CFLAR, SIAH2, DAPK3, MAP3K7, RIPK2, BCL2L11, BUB1, TRIAP1, CD5L, RAD21, OPA1, KIF1B, GREM1, BUB1B, TLR2, JAK2, GADD45B, NME6, TNFRSF21, PPP1R15A, PSMD10, STK17B, MFN2, UNC5C, GADD45G, AIFM1, CST3, IL1A, IL1B, RAF1, NR3C1, ITGB2, S100A8, PRKCB, CDK1, S100A9, CD14, LGALS1, PAEP, CTSH, BCL2, IRF1, IAPP, RALB, GJA1, IGFBP3, ERCC2, NFKB1, CAPN3, CDK11B, MAL, TNFAIP3, C5AR1, FGFR2, GADD45A, FAS, MT3, MAPK3, MAPK1, CASP1, PPP2R1A, TSPO, TIA1, AKT2, GRK5, ADRA1A, AHR, CHI3L1, TGFBR1, LTBR, TGFBR2, SNCA, BRCA1, MAP3K8, HTT, IER3, LGALS7, CASP4, COMP, SERPINB9, TNFSF10, FXR1, DAP, MAP2K6, RBM5, DAPK1, CTSC, YARS, CSE1L, CASP9, CASP6, PTEN, CXCR4, UBE2D3, PSME3, DAD1, POLR2G, RHOB, DYNLL1, EIF5A, RACK1, ACTC1, LCN2, DAB2, XIAP, MEF2A, PPARD, NOTCH2, ZBTB16, PRKCD, MEF2C, C1QBP, ZFP36L1, BAX, PPID, EP300, FOXO1, BNIP3, TIAM1, STK4, TRAF1, FADD, PAK2, ITGB3BP, BIRC3, SQSTM1, RIPK1, PMAIP1, C1D, GAS6, SEMA3A, ESPL1, MELK, CASP8, MEF2D, ARL6IP1, PEA15, PRKD1, RABEP1, DHCR24, RPS6KA1, SHB, TRADD, PDCD2, PKN2, MAPK14, PDCD4, PHLDA2, C3orf38, SFRP5, BCL2L15, STPG1, KANK2, ZFAND6, XAF1, JADE1, TCTN3, BRAT1, DRAM2, ADAMTSL4, RASSF6, RNF144B, C6orf120, PEG10, TAX1BP1, SGMS1, TRIM69, C19orf68, RNF130, TMEM219, SIAH1, SULF1, CCAR1, MRPL41, DDIAS, UNC5B, DRAM1, RNF152, PCSK9, RHBDD1, PPP1R13L, PDCD6IP, PRUNE2, PHLDA1, CKAP2, RASSF5, SLC5A11, CSRNP3, RFFL, ELMO1, INPP5D, BAD, TNFRSF25, RFK, MYDGF, TP53INP1, CYFIP2, PAWR, ITCH, CLPTM1L, NOX5, GSDMA, DLC1, CSRNP1, LITAF, CIB1, CITED1, HTATIP2, CDCA7, HINT2, BBC3, BEX2, CADM1, PEG3, CSRNP2, SEMA6A, PDCL3, GHITM, EGLN3, SUDS3, UBE2Z, AKTIP, BCL2L12, RRAGC, NEK6, TRIM39, SRA1, NGB, RTN4, DUSP22, GLRX2, TNFRSF19, RNF216, SLTM, BCLAF1, PAK7, SAP30BP, LGALS13, PUF60, FEM1B, FBXO10, TAOK2, TPX2, PYCARD, PLAGL1, BOK, FAF1, TRIM35, CDK11A, PRELID1, NISCH, EPB41L3, HIF3A, SH3GLB1, NOC2L

GO:0006919

BP

activation of cysteine-type endopeptidase activity involved in apoptotic process

Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.

HIP1, JAK2, PDCD6, AIFM1, NGF, TNF, S100A8, CCK, S100A9, NGFR, CTSH, HSPD1, F2R, FAS, CASP1, PPARG, SNCA, IFI27, CDKN1B, XDH, TNFSF10, DAP, VCP, BID, HSPE1, RACK1, CRADD, SMAD3, COL4A3, BAX, FADD, RIPK1, PMAIP1, CASP8, TRADD, PDCD2, RPS27L, ANP32B, BAD, FAM162A, DLC1, EGLN3, PYCARD, BOK

GO:0006921

BP

cellular component disassembly involved in execution phase of apoptosis

The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.

APC, BCAP31, CASP6, SATB1, PRKCQ, PTK2, PRKCD, CASP8, CAPN10, STK24

GO:0006924

BP

activation-induced cell death of T cells

A T cell apoptotic process that occurs towards the end of the expansion phase following the initial activation of mature T cells by antigen and is triggered by T cell receptor stimulation and signals transmitted via various surface-expressed members of the TNF receptor family such as Fas ligand, Fas, and TNF and the p55 and p75 TNF receptors.

FAS, AKT1, RPS6

GO:0006925

BP

inflammatory cell apoptotic process

Any apoptotic process in an inflammatory cell, any cell participating in the inflammatory response to a foreign substance e.g. neutrophil, macrophage.

FAS

GO:0006928

BP

movement of cell or subcellular component

The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.

WASL, DNALI1, ARPC2, ARPC3, SPINT2, MTSS1, JAK2, VNN1, HSPB1, IGF1, TPM3, TUBB, VIM, TPM1, CXCL8, TXN, CCL4, CD9, ANOS1, FPR2, CORO1A, LSP1, PTGS2, SERPINB5, STAT3, CAPZB, CD97, ARHGDIA, ARHGDIB, CAPZA1, ACTB, ACTR3, ACTR2, RAC1, ACTG1, TPM4, TUBB4B, MAP2K1, PLAUR, CALD1, ENPP2, MAPK14, ABI1, CHST4, MYLIP, ELMO1, ABI2, DNAH9, AMFR, TLN1, LYVE1

GO:0006929

BP

substrate-dependent cell migration

The orderly movement of a cell from one site to another along a substrate such as the extracellular matrix; the migrating cell forms a protrusion that attaches to the substrate.

ITGA2, VEGFC, ANKS1A, ITGA11

GO:0006930

BP

substrate-dependent cell migration, cell extension

The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.

SDCBP, CTTN

GO:0006931

BP

substrate-dependent cell migration, cell attachment to substrate

The formation of adhesions that stabilize protrusions at the leading edge of a migrating cell; involves integrin activation, clustering, and the recruitment of structural and signaling components to nascent adhesions.

TNFRSF12A

GO:0006933

BP

negative regulation of cell adhesion involved in substrate-bound cell migration

The disassembly of adhesions at the front and rear of a migrating cell. At the leading edge, adhesion disassembly accompanies the formation of new protrusions; at the cell rear, it promotes tail retraction.

ITGB1BP1, SNAI2, PTPRC

GO:0006935

BP

chemotaxis

The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).

CYR61, CXCL14, PLAU, FGF2, CXCL1, CXCL8, CCL3, RNASE2, RALA, CCL2, CCL5, RAC2, FOSL1, CXCL2, TYMP, S1PR1, FPR1, C5AR1, ANOS1, CXCR2, FPR2, PTAFR, MAPK1, LSP1, PIK3CB, CXCL5, CXCL12, CCL20, CCL8, CXCL6, MAP2K1, PLAUR, PLD1, ENPP2, RALBP1, MAPK14, AMOT, CMTM8, DOCK2, CMTM3, RARRES2, CXCL16, PLGRKT, ACKR4, ZNF580

GO:0006936

BP

muscle contraction

A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.

FXYD1, SORBS3, NDUFS6, HSBP1, CRYAB, TPM3, TPM2, TPM1, CHRNB1, MYL6B, GJA1, CKMT2, DES, ITGB5, MYL12A, MYL9, TMOD1, LMOD1, OXTR, MYH11, GJC1, SLC6A8, EMD, MYL6, CALM2, ACTA2, ACTG2, TPM4, MYL7, MYL5, CALD1, ASPH, SNTA1, SNTB1, KCNJ12, SSPN, SLMAP, MYLK, PABPN1, TTN, STAC, SORBS1, KCNIP2, MYOT, MYH2, TLN1, MYH4

GO:0006937

BP

regulation of muscle contraction

Any process that modulates the frequency, rate or extent of muscle contraction.

PPP1R12B, ANXA6, TPM1, MYL9, MYL5, KCNA1

GO:0006939

BP

smooth muscle contraction

A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.

ROCK2, CHRM3, EDNRA, HTR7, ADRA1A, MYH11, SMTN, PDE4D, MYLK, TPCN2

GO:0006940

BP

regulation of smooth muscle contraction

Any process that modulates the frequency, rate or extent of smooth muscle contraction.

DAPK3, CHRM2, ADRA2B, TNNI3, NMU, ATP1A2, CNN1, CAV1