GO:0000002

BP

mitochondrial genome maintenance

The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.

OPA1, SLC25A4, MPV17, MEF2A, SLC25A36, MGME1, PIF1, MRPL17, AKT3

GO:0000010

MF

trans-hexaprenyltranstransferase activity

Catalysis of the reaction: all-trans-hexaprenyl diphosphate + isopentenyl diphosphate = all-trans-heptaprenyl diphosphate + diphosphate.

PDSS1, PDSS2

GO:0000012

BP

single strand break repair

The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.

TDP1

GO:0000014

MF

single-stranded DNA endodeoxyribonuclease activity

Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.

ERCC1, MRE11A, RAD50, ERCC4, DCLRE1C

GO:0000015

CC

phosphopyruvate hydratase complex

A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.

ENO1, ENO2, ENO3

GO:0000016

MF

lactase activity

Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose.

LCT

GO:0000018

BP

regulation of DNA recombination

Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic 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.

IL7R, KPNA2, KPNA1, ALYREF, SMARCAD1

GO:0000019

BP

regulation of mitotic recombination

Any process that modulates the frequency, rate or extent of DNA recombination during mitosis.

MRE11A, RAD50

GO:0000022

BP

mitotic spindle elongation

The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.

PRC1, KIF23

GO:0000023

BP

maltose metabolic process

The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch.

MGAM, GAA

GO:0000026

MF

alpha-1,2-mannosyltransferase activity

Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->2) linkage.

ALG9

GO:0000027

BP

ribosomal large subunit assembly

The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.

RPL10, RPL12, RPL5, RPL23A, RPL11, RPL24, MDN1, MRTO4

GO:0000028

BP

ribosomal small subunit assembly

The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit.

RPS17, RPSA, RPS27, RPS5, RPS10, RPS14, RPS27L, RRP7A

GO:0000030

MF

mannosyltransferase activity

Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid.

DPY19L2, DPY19L3, DPY19L4, ALG9, POMT1

GO:0000033

MF

alpha-1,3-mannosyltransferase activity

Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->3) linkage.

ALG8

GO:0000036

MF

ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process

Interacting selectively and non-covalently with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP) as part of the process of fatty acid biosynthesis.

NDUFAB1

GO:0000038

BP

very long-chain fatty acid metabolic process

The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22.

HSD17B4, ACOX1, ACOT4, SLC27A6

GO:0000042

BP

protein targeting to Golgi

The process of directing proteins towards the Golgi; usually uses signals contained within the protein.

GOLGA4, TRIP11, SORL1, GOLGA1, OPTN

GO:0000045

BP

autophagosome assembly

The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.

ATG13, ATG12, PSEN1, GABARAPL2, RAB1A, WIPI1, KIAA1324, TP53INP2, ATG16L2, RB1CC1, TP53INP1, ATG2B, MAP1LC3B, GABARAPL1, MAP1LC3A, RAB23, WDR45, WIPI2

GO:0000049

MF

tRNA binding

Interacting selectively and non-covalently with transfer RNA.

PTCD1, TRMU, FARS2, SSB, RPL35A, RARS, YARS, EEF1A1, NSUN2, IFIT5, KARS, EARS2, TRMT1L, TRNT1, THUMPD3, SEPSECS, EIF2AK4, FARSA

GO:0000050

BP

urea cycle

The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.

ASS1, CAD, SLC25A15

GO:0000052

BP

citrulline metabolic process

The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins.

DDAH1, DDAH2, ASS1

GO:0000053

BP

argininosuccinate metabolic process

The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate.

ASS1

GO:0000054

BP

ribosomal subunit export from nucleus

The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.

EIF6, ABCE1

GO:0000055

BP

ribosomal large subunit export from nucleus

The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.

XPO1, RRS1, NUP88, SDAD1

GO:0000056

BP

ribosomal small subunit export from nucleus

The directed movement of a ribosomal small subunit from the nucleus into the cytoplasm.

XPO1, NUP88

GO:0000059

BP

protein import into nucleus, docking

A protein complex assembly process that contributes to protein import into the nucleus, and that results in the association of a cargo protein, a carrier protein such as an importin alpha/beta heterodimer, and a nucleoporin located at the periphery of the nuclear pore complex.

IPO5, TNPO2, RANBP6, KPNB1, IPO4, NUP205

GO:0000060

BP

protein import into nucleus, translocation

A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.

IPO5, TNPO2, RANBP6, TGFB1, TNF, BCL3, MT3, AKT1, BCL6, AKR1C3, SLC11A1, NUTF2, POLA2, KPNB1, CEP57, IPO4, PHB2, RBM22

GO:0000062

MF

fatty-acyl-CoA binding

Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.

ACOT7, ACOX3, ECI2, SCP2, SOAT1, HMGCL, ACADSB, ACADVL, ALDH6A1, ACOX1, ACBD5, ACOX2, ACBD3

GO:0000064

MF

L-ornithine transmembrane transporter activity

Enables the transfer of L-ornithine from one side of a membrane to the other. L-ornithine is 2,5-diaminopentanoic acid.

SLC25A15

GO:0000066

BP

mitochondrial ornithine transport

The directed movement of ornithine, 2,5-diaminopentanoic acid, into, out of or within a mitochondrion.

SLC25A15

GO:0000070

BP

mitotic sister chromatid segregation

The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.

NDC80, ZNF207, BUB3, ZWINT, CENPA, NEK2, PLK1, MAD2L1, ESPL1, SMC1A, CEP57, KIF18B, SPAG5, KIFC1, NUSAP1, DSN1, SMC4, KNSTRN

GO:0000075

BP

cell cycle checkpoint

A cell cycle process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction.

FANCG, CCNE2, RB1, CCNG2, ZAK

GO:0000076

BP

DNA replication checkpoint

A cell cycle checkpoint that prevents the initiation of nuclear division until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.

DNA2, RAD9B, RAD9A, CDC6, TIPIN, CDT1

GO:0000077

BP

DNA damage checkpoint

A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.

CHEK1, RAD1, NBN, H2AFX, E2F1, PTPN11, PEA15, MAPK14, ATRIP, USP28, RAD9A, RHNO1, INTS7, ZAK

GO:0000079

BP

regulation of cyclin-dependent protein serine/threonine kinase activity

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

CCNT1, CCNT2, DIRAS3, CCNE2, CCNA2, GADD45A, CDC25A, CDC25C, SFN, GTF2H1, CDKN1A, CDKN2B, CDKN2C, CDKN1B, CDK7, CCNG1, BLM, PTEN, CDC37, CDKN3, PKMYT1, CDC6, BCCIP

GO:0000082

BP

G1/S transition of mitotic cell cycle

The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.

CDC7, PPP6C, ORC5, LATS1, CCNE2, DHFR, TYMS, ITGB1, RB1, CDK1, EIF4E, INHBA, POLA1, CDK4, PCNA, GSPT1, RCC1, CDK2, MCM3, CDC25A, RRM2, MCM4, MCM5, MCM7, RPA3, ACVR1B, CDKN1A, CDKN2C, RANBP1, CDKN1B, ID4, CDC34, PRIM1, PRIM2, MCM2, CDK7, BCAT1, POLE2, RPS6, CCNA1, CDK3, CDK6, ACVR1, PPAT, POLE, PPP3CA, SKP2, ORC1, EIF4EBP1, CAMK2D, CUL2, CUL3, CUL4A, POLA2, MCM6, CDKN3, RHOU, MCM10, IQGAP3, CACUL1, CRLF3, CUL5, CDCA5, PKMYT1, CDC6, CDT1, LATS2, PLK2, ORC3, DBF4, MCM8, FBXO5, ORC6

GO:0000083

BP

regulation of transcription involved in G1/S transition of mitotic cell cycle

Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.

BACH1, BRD4, DHFR, TYMS, RB1, CDK1, POLA1, PCNA, RRM2, CCNA1, ORC1, NPAT, CDC6, CDT1, FBXO5

GO:0000086

BP

G2/M transition of mitotic cell cycle

The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.

PLK4, CHEK1, AURKA, PPP1R12A, ENSA, SSNA1, PPP1R12B, HMMR, OFD1, HAUS5, CEP152, CCNB2, PCNT, LATS1, TUBB4A, CDK1, TUBB, HSP90AA1, UBC, CCNB1, PRKACA, TUBG1, CDK2, PPP2R1A, WEE1, CDC25A, CDC25B, CDC25C, PRKAR2B, CDKN1A, CDKN2B, NES, CSNK1D, CSNK1E, CDK7, NEK2, PLK1, ARPP19, PPP1CB, CALM2, YWHAE, RPS27A, UBA52, DYNLL1, SKP1, TUBA4A, TUBB4B, KHDRBS1, FOXM1, SKP2, DYNC1I2, DCTN2, CKAP5, DCTN1, DYNC1H1, MELK, PCM1, MAPRE1, TPD52L1, ODF2, CEP78, CEP135, BORA, TUBA1A, HAUS6, SDCCAG8, CEP57, CEP70, PHLDA1, HAUS1, OPTN, MASTL, AJUBA, PKMYT1, HAUS7, FBXL15, HAUS4, CSRP2BP, CENPJ, PLCB1, HAUS2, NDE1, FBXL7, TPX2, BTRC

GO:0000095

MF

S-adenosyl-L-methionine transmembrane transporter activity

Enables the transfer of S-adenosylmethionine from one side of a membrane to the other. S-adenosylmethionine is S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.

SLC25A26

GO:0000096

BP

sulfur amino acid metabolic process

The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.

AHCY, GCLC, GCLM, MTR

GO:0000097

BP

sulfur amino acid biosynthetic process

The chemical reactions and pathways resulting in the formation of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine.

CDO1

GO:0000098

BP

sulfur amino acid catabolic process

The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine.

CTH

GO:0000103

BP

sulfate assimilation

The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.

PAPSS2, TXN, TXN2

GO:0000104

MF

succinate dehydrogenase activity

Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.

SDHB, SDHA, SDHC

GO:0000105

BP

histidine biosynthetic process

The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

MTHFD1, MTHFD2L

GO:0000109

CC

nucleotide-excision repair complex

Any complex formed of proteins that act in nucleotide-excision repair.

ERCC1, POLD1, ERCC4

GO:0000110

CC

nucleotide-excision repair factor 1 complex

One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively.

ERCC1, XPA, ERCC4

GO:0000111

CC

nucleotide-excision repair factor 2 complex

One of several protein complexes involved in nucleotide-excision repair; possesses damaged DNA binding activity. In S. cerevisiae, it is composed of Rad4p and Rad23p.

XPC

GO:0000117

BP

regulation of transcription involved in G2/M transition of mitotic cell cycle

Any process that regulates transcription such that the target genes are transcribed as part of the G2/M transition of the mitotic cell cycle.

BACH1

GO:0000118

CC

histone deacetylase complex

A protein complex that possesses histone deacetylase activity.

SAP18, HDAC3, TBL1X, ZNF217, NCOR1, TAL1, CBX5, NRIP1, HINT1, HDAC4, HDAC1, HDAC7, HDAC8, TBL1XR1, DNTTIP1, RERE, HDAC6, HDAC9, HDAC5, NCOR2

GO:0000120

CC

RNA polymerase I transcription factor complex

A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase I.

CD3EAP, TAF1C, TAF1A

GO:0000122

BP

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.

E2F8, CNOT1, AHRR, SUPT5H, WWP2, ZNF593, ARID1A, BHLHE40, BACH1, XPO1, SMAD7, MDM4, HDAC3, FOXP2, PER1, PAX4, HOXA2, KLF4, FOXO3, SNAI2, TCF21, SOX15, PARK2, ZEB2, KDM1A, SORBS3, SHOX2, TBL1X, MITF, SIN3B, ZNF217, H2AFY, NCOR1, MAF, HSBP1, USP2, ZNF189, PSMD10, URI1, DKK1, TRIM37, HEXIM1, ZNF205, ZBTB7A, CBX7, MBD3, WHSC1, MYC, TGFB1, PTH, TNF, ESR1, TP53, EDN1, NFIC, HMGB1, PARP1, UBC, GLI2, GLI3, HIST1H1E, NR2F1, TXN, FGFR1, VDR, ESRRA, TPR, BMP2, BMP4, SKI, SKIL, HCLS1, ETS2, EZR, VEGFA, HIVEP1, TCF3, GCFC2, HIST1H1C, CD36, JUNB, JUND, TAL1, DDX5, EGR1, ATF3, WT1, NFKB1, FST, NR1D1, EFNA1, FGFR2, BMP6, HNRNPA2B1, SFPQ, SP100, NR2F2, YY1, DNMT1, ZFP36, CALR, MZF1, RBL1, KDM5A, FGF9, CTNNB1, PHB, DDIT3, SOX6, SREBF1, PPARG, ZEB1, SNCA, IFI27, STAT3, ID1, LEP, BCL6, NR4A2, NKX2-1, NOTCH1, ID4, RFX5, NRIP1, PSEN1, CDKN1C, ERF, ASCL1, SMARCA2, SMARCA4, NR0B1, HDGF, ZNF136, HMGA2, PLK1, FOSB, ATN1, NR1H2, HDAC4, CTBP2, FOXL2, UBE2D3, PKIA, RPS14, RPS27A, UBA52, UBE2I, YBX1, IGBP1, BTG2, HAMP, SMAD3, VLDLR, HSF1, MDM2, E2F1, INSM1, RELB, DR1, SATB1, POU5F1, MEF2A, ID2, SP3, ID3, HHEX, CAV1, PPARD, RELA, TLE1, REL, MXD1, ZBTB16, MEF2C, GABPA, C1QBP, DLX2, PPARA, FOXM1, AES, PPID, EP300, SREBF2, FOXO1, DLG1, KLF10, NR1H3, MAP2K5, GPS2, TRIM28, IKZF1, NFATC2, SMAD4, SQSTM1, HDAC1, TDG, CUL3, PTCH1, ACVR2B, RUNX3, CUX1, SIM2, HES1, MXD4, ZNF345, ZNF268, CHD4, ARID5B, DRAP1, SUZ12, TCEAL1, ZMYND11, ANKRD1, NR0B2, NCOA2, TWIST1, SMAD2, EZH2, ZFHX3, CRY1, NFIL3, IFI16, BRMS1L, KANK2, WWC2, OTUD7B, NIPBL, ZNF280D, ATF7IP, NFXL1, TSHZ1, CXXC5, MTDH, JAZF1, ZNF280B, GATAD2A, TMPRSS6, MINA, AEBP1, WWC1, SIRT2, ZNF567, NKAP, EID2, CPEB3, GLIS3, TRPV1, FLCN, SMARCC2, OSR1, ZNF564, ZNF675, FNIP1, PPP1R13L, HDAC7, ZFPM2, JDP2, RTF1, NR4A3, ESR2, HDAC2, PROX1, CREBBP, N4BP2L2, GATA6, AURKB, HES6, AJUBA, PAWR, RITA1, EHMT2, PRMT6, NEDD4L, PURB, PHF12, NR1H4, CIC, TRIB3, ZNF382, SPEN, UHRF1, TSC22D3, MNT, MDFI, CITED2, HOPX, TCF25, DUSP26, HDAC8, BACH2, TBL1XR1, FOXP3, PEG3, ZNF350, BCL11A, EPC1, HIPK2, TXNIP, FZD8, SUV39H2, SOX17, SUDS3, SMURF2, TRPV4, TAF9B, ZBTB20, CHD8, HMG20A, HEYL, TCF7L2, KMT5A, DLL4, TSHZ2, DUSP22, RLIM, DACT1, LMCD1, H2AFY2, ZBTB4, FNIP2, RCOR3, RERE, IMPACT, DNMT3B, UXT, MLX, TRPS1, DDX20, DACH1, MOSPD1, HDAC9, ZHX1, WWC3, YEATS2, SUFU, TIMELESS, TRIM33, DICER1, HDAC5, ZNF148, PKIG, NOC2L, MTF2, NFE2L3, HEY1, HCFC2, NCOR2, EID1

GO:0000123

CC

histone acetyltransferase complex

A protein complex that possesses histone acetyltransferase activity.

OGT, IKBKAP, EP300, JADE1, JADE3, CREBBP, ELP4, PHF20, ELP3, KANSL3

GO:0000124

CC

SAGA complex

A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8.

USP27X, SUPT3H, TADA3, USP34, USP51, TAF9B, ENY2, USP22

GO:0000125

CC

PCAF complex

A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs.

TADA2A, TAF10, KAT2B, TRRAP

GO:0000127

CC

transcription factor TFIIIC complex

A heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions.

GTF3C2, GTF3C4

GO:0000132

BP

establishment of mitotic spindle orientation

A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.

NDC80, SPRY2, SPRY1, HTT, CENPA, DYNLT1, GPSM2, ARHGEF2, SPDL1, NDEL1, NDE1

GO:0000137

CC

Golgi cis cisterna

The Golgi cisterna closest to the endoplasmic reticulum; the first processing compartment through which proteins pass after export from the ER.

GOLGA2, NECAB3, TMEM59

GO:0000138

CC

Golgi trans cisterna

The Golgi cisterna farthest from the endoplasmic reticulum; the final processing compartment through which proteins pass before exiting the Golgi apparatus; the compartment in which N-linked protein glycosylation is completed.

B4GALT1, SGMS1, HID1, TMEM59

GO:0000139

CC

Golgi membrane

The lipid bilayer surrounding any of the compartments of the Golgi apparatus.

GPR89A, SLC33A1, GOLIM4, EBAG9, PPP6C, COPE, AP3D1, GOSR2, ANKRD28, LEPROT, SURF4, GRM6, TLR3, B4GALT5, B4GAT1, KDELR3, CYTH3, STX6, B3GALT2, HS6ST1, TPST1, B4GALT4, TPST2, FAM20B, ENTPD6, VAMP4, SEC22B, AP1G2, TRAPPC6A, SEC24D, SEC31A, CLSTN1, CSPG5, TNKS, VAPB, SNAPIN, LARGE, SNAP29, B3GALT4, F8, EGFR, SERPINA1, NRAS, PDGFB, TGFA, INS, HLA-B, HLA-DRA, HLA-DQA2, HLA-DQA1, HLA-DQB1, PDGFA, CD74, CYP2E1, CD55, FURIN, GPR89B, TRAPPC2, SRGN, SLC2A1, F5, NCAM1, HLA-E, HLA-DRB4, B4GALT1, FOLR1, AREG, ST6GAL1, GJA1, HLA-G, ATF6, HLA-DPA1, OSBP, FUT4, KDELR1, NOS3, HLA-A, HLA-F, GBP1, GBP2, MAN1A1, BSG, TRIM23, SREBF1, IFNGR2, PRKCI, NSG1, NSF, NOTCH1, ARCN1, TRAPPC10, CSNK1D, PITPNB, MAN2A2, TMED10, PSEN1, PSEN2, CAV2, CLCN3, CLCN5, NDST1, ARFIP1, COPA, CTSC, EMP2, SEC13, AP1S2, GABARAPL2, CDC42, RAB2A, ST8SIA6, B2M, COPZ1, AP1S1, RAB1A, RAC1, SLC35A2, SLC35A1, HLA-DRB3, TMF1, ARF1, PKD1, ATP2C1, CAV1, NOTCH2, ICA1, GOLGA2, MGAT2, GALNT2, GALNT1, AP1B1, ST3GAL1, ST3GAL3, ST3GAL4, SREBF2, HYAL2, MALL, CLN3, PLD1, GOLGA4, SERINC3, CUL3, CUX1, COG2, TMED2, RHEB, DHCR24, SEC23A, TRIP11, EXT1, UGCG, ST3GAL2, TMEM132A, HLA-DRB5, GNPTAB, MGAT5B, KLHL12, WIPI1, MANEA, ARHGAP21, WLS, STEAP4, RAB12, RHBDD2, AGTRAP, PARM1, C6orf89, B3GNT9, CHSY3, SLC35D2, RHOU, LPCAT2, CHST15, HS2ST1, CHST3, GALNT5, GALNT7, GALNT10, SGMS1, CHSY1, GPSM1, ERC1, ZDHHC17, TRAPPC5, HACE1, KIAA0319L, DSEL, GCNT2, GALNT15, GALNT4, ARFGAP2, CHST4, B3GNT7, SVIP, MCFD2, TMEM167A, CSGALNACT1, PXYLP1, RAB2B, ABCA5, ST8SIA4, GBF1, TFG, GLG1, EXT2, PMEPA1, ERGIC1, RHBDF1, OPTN, GALNT14, PGAP3, SEC16B, ST6GAL2, HS6ST2, GPER1, MPHOSPH9, PKMYT1, CHP1, SH3GL2, SLC35A5, NDFIP1, PDCD10, APOO, ST6GALNAC5, TAPBPL, TMEM59, FUT8, B3GNT5, PDGFD, CHST5, CHST6, GBP3, RAB1B, LMAN2L, XYLT2, BLZF1, TNKS2, ACBD3, CLSTN2, ST6GALNAC4, GLIPR2, NAA60, RNF121, FKRP, GBA2, GOPC, ABCB6, ARFGAP3, PNPLA8, CHST11, MAN1C1, PDGFC, RAB6B, AGPAT3, CHST7, NDFIP2, SYBU, SMPD4, ZDHHC7, B3GNT2, BET1L, VAPA, PI4KB, CTSZ, B4GALT6, SCOC, ST6GALNAC2, GNPTG, DSE, TMCO1, MGAT4A, BOK, PPP6R1, MAPK8IP3, MGAT4B, RNF24, ST3GAL6, ITM2B, SLC35A3, PIKFYVE, COG6, SH3GLB1, GOLT1B, TMED3, CHST2, TRAPPC1, HS3ST3B1, COPG1, ARFGEF2

GO:0000145

CC

exocyst

A protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse. At least eight complex components are conserved between yeast and mammals.

WASH1, EXOC5, EXOC3, RALB, TNFAIP2, SEPT2, MYRIP, STXBP6, EXOC4, EXOC2, EXOC1, EXOC7

GO:0000146

MF

microfilament motor activity

Catalysis of movement along a microfilament, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).

MYO1C, MYO1D, MYH9, MYO1E, MYO9B, MYH2, MYO5B, MYO5A, MYH4

GO:0000149

MF

SNARE binding

Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.

GOSR2, STX7, EXOC3, VAMP4, SEC22B, STX11, SNAPIN, SYT1, STX2, VAMP7, GABARAPL2, STXBP1, VAMP2, TNFAIP2, STX4, STX3, VAMP3, SEC22A, ANKRD27, TRIM9, CAPN10, VTI1B

GO:0000150

MF

recombinase activity

Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.

RAD51C, RAD51D, RAD51

GO:0000151

CC

ubiquitin ligase complex

A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

ASB14, WWP2, GPR37, MED7, PARK2, FBXO24, RNF8, UBE4B, HSPA1A, HSPA1B, DNAJA1, BRCA1, BRCC3, RNF144A, UBE2E1, UBE2V1, MED21, RNF19B, UBR3, CBLL1, RNF144B, CAND1, UBR1, UBE2J2, FBXO25, DCUN1D4, DYRK2, MED12, MIB2, DCUN1D1, MED30, GMCL1, ASB16, MPHOSPH8, BARD1, PINK1, WWP1, MED20, SMURF2, FBXO8, RNF19A, MED17, RNF216, RNF14, FBXL7, FBXO10, FBXO9, STUB1, SUGT1, ARIH1, ASB3

GO:0000152

CC

nuclear ubiquitin ligase complex

A ubiquitin ligase complex found in the nucleus.

BRCC3

GO:0000154

BP

rRNA modification

The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.

NOP56

GO:0000155

MF

phosphorelay sensor kinase activity

Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.

KCNH2

GO:0000159

CC

protein phosphatase type 2A complex

A protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit.

PPP2R1A, PPP2CB, CYCS, PPP2R3A, STRN3, PPP2R5C, PPP2R5D, PPP2R5A, PPP2R5B, PPP2R4, STRN4

GO:0000160

BP

phosphorelay signal transduction system

A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.

KCNH2

GO:0000164

CC

protein phosphatase type 1 complex

A protein complex that possesses magnesium-dependent protein serine/threonine phosphatase (AMD phosphatase) activity, and consists of a catalytic subunit and one or more regulatory subunits that dictates the phosphatase's substrate specificity, function, and activity.

PPP1R11, PPP1R15A, PPP1R2, PPP1CA, PPP1CB, PPP1R3B

GO:0000165

BP

MAPK cascade

An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.

PSMD11, PSMD12, EREG, MAPK13, PSMD3, RASA4, JAK2, PSMD10, PAK3, FGF18, FGF19, EGFR, MYC, NRAS, KRAS, PDGFB, TGFB1, INS, TNF, IL1B, RAF1, PDGFA, ERBB2, FYN, FGF2, PDGFRB, UBC, CCL3, KIT, FGFR1, CCL2, CCL5, SCG2, NCAM1, PDGFRA, PSMC3, PSMB1, EFNA1, RASA1, KITLG, FGF7, FGFR2, ERBB3, JAK1, PSMA1, PSMA2, PSMA3, PSMA4, ZFP36, MAPK3, PSMB8, PSMB9, PSMB4, PSMB5, MAPK1, PEBP1, FGF9, YWHAB, BTC, IRS1, ACTN2, PSMC2, MAP2K2, PSMB10, PSMC4, MAPKAPK2, PSMB3, PSMD7, JAK3, MAP2K6, NDST1, MAP3K7CL, PSME3, CALM2, PSMC1, PSMC6, RBX1, RPS27A, UBA52, GRB2, DLG4, SHC2, SPTBN1, IL5RA, MEF2A, NRG1, MAP2K1, TEK, CAV1, PTK2, MEF2C, ZFP36L1, SOS1, GRIN2A, MAPK7, PSMD2, CAMK2D, CUL3, IL18, RASA3, MEF2D, PSME4, PEA15, RASA2, ERBB4, ANGPT1, SMAD1, DUSP5, DUSP6, DUSP7, SETX, SPRED1, PABPN1, FRS2, FGF13, SYNGAP1, HBEGF, MAP3K5, DUSP9, SPTBN4, TAOK3, DOK5, NLK, KL, LAMTOR3, LAMTOR2, IRS2, MAP3K4

GO:0000166

MF

nucleotide binding

Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

RBM47, IGF2BP3, HNRNPDL, U2SURP, SYNJ2, POLR2D, RBFOX2, HNRNPR, SYNJ1, ORC5, SYNCRIP, REV3L, SRSF10, CRCP, DHRS3, DXO, TMEM63A, SCAF4, CELF2, PARN, CNOT4, PTBP3, TYMS, SSB, HSP90AA1, HNRNPC, SNRPA, HNRNPA1, POLA1, PYGM, HNRNPL, NT5E, HNRNPA2B1, SFPQ, EIF4B, PTBP1, POLD1, RBMS1, TIA1, HNRNPH3, HNRNPH1, FUS, RBMX, MATR3, VDAC2, RBM25, HINT1, FHIT, HDGF, HNRNPA3, HNRNPM, RBM5, RCAN1, HNRNPH2, EIF3B, RPL23A, TRA2B, RBM6, GPSM2, RBM3, SRSF2, EWSR1, SRSF11, POLE, SRSF1, GRSF1, TARDBP, SRSF9, SRSF5, SRSF6, TRA2A, CIRBP, HNRNPD, RBM39, ELAVL3, ZNF638, SART3, NONO, RNPS1, RBMS2, ELAVL1, CRY1, MRPL23, SNRNP35, CPEB4, LARP7, PABPC1L, NCBP3, RBM48, RBM26, SLC27A4, SLC27A1, RBPMS2, RBM43, LARP4, NOL8, CPEB2, PABPN1, ALYREF, CHD1L, PPARGC1B, RBM45, TNRC6A, CPEB3, NUP35, ZCRB1, ENOX1, PPIL4, SREK1, PSPC1, TAF15, RBPMS, MSI2, DAZAP1, RBM33, RBM17, RNPC3, RBM15, SPEN, HNRNPAB, CDC6, RBM4B, LARP6, RBM4, RBM24, HINT2, POLDIP3, NIFK, SLIRP, RBM38, UPF3A, PABPC3, ESRP2, TNRC6C, RAVER2, NOX4, HINT3, PRTFDC1, RBM22, RBFOX1, SLTM, TRNAU1AP, AKAP7, MYEF2, PPARGC1A, NXF1, PUF60, PTBP2, G3BP2, PPIE, SCAF8, TNRC6B, VDAC3, SLC27A6, LEMD3, RBMX2, RRP7A, SF3B6, R3HCC1, KIAA0430, RBM8A, IGF2BP2

GO:0000171

MF

ribonuclease MRP activity

Catalysis of the site-specific cleavage of RNA by a catalytic RNA-mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA.

POP4

GO:0000172

CC

ribonuclease MRP complex

A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication.

POP4

GO:0000175

MF

3'-5'-exoribonuclease activity

Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.

EXOSC9, EXOSC2, EXOSC7, PNPT1, ISG20, EXOSC4, EXOSC3, CNOT7, DIS3, REXO2

GO:0000176

CC

nuclear exosome (RNase complex)

A ribonuclease complex that has 3-prime to 5-prime processive and distributive hydrolytic exoribonuclease activity and endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

EXOSC9, EXOSC2, C1D, EXOSC7, EXOSC6, EXOSC8, EXOSC4, EXOSC3, DIS3

GO:0000177

CC

cytoplasmic exosome (RNase complex)

A ribonuclease complex that has 3-prime to 5-prime processive hydrolytic exoribonuclease activity producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

EXOSC9, EXOSC2, EXOSC7, EXOSC6, EXOSC8, EXOSC4, EXOSC3, DIS3, CARHSP1

GO:0000178

CC

exosome (RNase complex)

A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

SKIV2L2, EXOSC9, EXOSC2, EXOSC7, EXOSC6, KHSRP, EXOSC8, EXOSC4, EXOSC3, DIS3

GO:0000179

MF

rRNA (adenine-N6,N6-)-dimethyltransferase activity

Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.

DIMT1

GO:0000182

MF

rDNA binding

Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA.

H2AFY, TSPYL2

GO:0000183

BP

chromatin silencing at rDNA

Repression of transcription of ribosomal DNA by altering the structure of chromatin.

SMARCA5, HIST1H4A, HIST1H3D, H3F3A, SIRT2

GO:0000184

BP

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.

CTIF, PARN, RPLP1, RPLP2, RPLP0, RPS17, RPSA, GSPT1, RPS2, RPL35A, RPL7, RPL17, RPS4Y1, RPL13, RPL10, RPL12, PPP2R1A, RPL22, RPL4, RPL13A, RPS27, RPL35, RPL27A, RPL5, RPL21, RPL28, RPS9, RPS5, RPS10, RPL29, RPL34, RPL14, RPS20, RPS3A, RPL26, RPL15, RPL27, RPL37A, RPL37, RPS7, RPS8, RPS15A, RPS16, RPS14, RPS18, RPS13, RPS11, RPL7A, RPL23A, RPS6, RPS25, RPS26, RPL30, RPL31, RPL10A, RPL32, RPL11, RPL41, RPS27A, UBA52, RPL38, RPS21, RPL24, RPL36A, RPL19, RPL18A, RPL18, NCBP1, RNPS1, DCP2, SMG8, UHMK1, SMG1, UPF3A, UPF2, PNRC2, SMG5, RPL36, RBM8A

GO:0000185

BP

activation of MAPKKK activity

Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK).

GADD45B, GADD45G, TNF, GADD45A, TAB1, MAP4K3, MAP4K5

GO:0000186

BP

activation of MAPKK activity

The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).

MAP3K13, MAP3K7, JAK2, GADD45B, EGFR, NGF, RAF1, NTRK1, GNAI2, BMP4, F2R, ADORA1, TGFBR1, MAP3K8, CRKL, PSEN1, MAP3K7CL, RAP1A, ADAM9, RAPGEF1, CARTPT, MLK4, FRS2, MAP3K5, ZAK, LAMTOR3, TAOK2, KIDINS220, LAMTOR2, MAP3K4

GO:0000187

BP

activation of MAPK activity

The initiation of the activity of the inactive enzyme MAP kinase (MAPK).

TLR4, IRAK2, MAP3K7, RIPK2, PAK3, TGFA, TNF, IL1B, CD74, IGF1, INSR, CDK1, THBS1, FGF2, UBC, SAA1, KIT, GHR, BMP2, TDGF1, HGF, EFNA1, FPR1, C5AR1, MAPK3, MAPK1, ADORA2B, ERP29, MAP2K2, CHRNA7, WNT5A, PIK3CB, MAPKAPK2, IRAK1, MAP2K6, CD81, CXCR4, RPS27A, UBA52, SHC2, NRG1, MAP2K1, PTPN11, MAP2K5, PEA15, TAB1, MAPK14, DUSP5, DUSP6, DUSP7, AVPI1, CSPG4, IQGAP3, MUC20, TAB3, FRS2, DUSP9, GHRL

GO:0000188

BP

inactivation of MAPK activity

Any process that terminates the activity of the active enzyme MAP kinase.

DUSP1, PPP2R1A, RGS3, RGS4, DUSP3, CAV1, DUSP2, DUSP8, GPS2, DUSP5, DUSP6, DUSP7, SPRED1, DUSP18, DUSP9, DUSP16, DUSP21, DUSP22, DUSP10

GO:0000189

BP

MAPK import into nucleus

The directed movement of a MAP kinase to the nucleus upon activation.

TPR, MAPK3, MAPK1

GO:0000209

BP

protein polyubiquitination

Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.

TMEM129, PSMD11, PSMD12, PSMD3, SIAH2, PARK2, PSMD10, UBR5, UBE4B, TNKS, UBC, BCL2, PSMC3, PSMB1, PSMA1, PSMA2, PSMA3, PSMA4, PSMB8, PSMB9, PSMB4, PSMB5, TPP2, PSMC2, PSMB10, PSMC4, CDC34, UBE2A, PSMB3, RNF144A, PSMD7, UBE2E1, NPEPPS, UBE2D3, PSME3, PSMC1, PSMC6, RBX1, RPS27A, UBA52, UBE2B, SKP1, CBLB, PSMD2, SKP2, PPIL2, UBE2V1, CUL3, BLMH, CBFB, PSME4, SHPRH, UBE3C, UBE2V2, LONRF1, MARCH8, HECTD2, FBXO31, RNF19B, RNF111, RNF165, RNF144B, RBBP6, HUWE1, TRIM69, SIAH1, UBE2J2, FBXO22, MARCH1, MYLIP, MIB2, NEDD4L, RNF126, TRIM6, TNKS2, SMURF2, RC3H2, RNF19A, RLIM, DTL, RNF181, KLHL42, HDAC6, RNF14, MKRN1, LNPEP, AMFR, PRPF19, STUB1, RNF24, BTRC, ARIH1, RNF114

GO:0000212

BP

meiotic spindle organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle.

AURKA, TUBG1, MYH9, ESPL1

GO:0000213

MF

tRNA-intron endonuclease activity

Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.

TSEN15

GO:0000215

MF

tRNA 2'-phosphotransferase activity

Catalysis of the reaction: 2'-phospho-[ligated tRNA] + NAD+ = mature tRNA + ADP ribose 1'',2''-phosphate + nicotinamide + H2O. This reaction is the transfer of the splice junction 2-phosphate from ligated tRNA to NAD+ to produce ADP-ribose 1'-2' cyclic phosphate.

TRPT1

GO:0000220

CC

vacuolar proton-transporting V-type ATPase, V0 domain

The V0 domain of a proton-transporting V-type ATPase found in the vacuolar membrane.

TCIRG1, ATP6V0A1

GO:0000221

CC

vacuolar proton-transporting V-type ATPase, V1 domain

The V1 domain of a proton-transporting V-type ATPase found in the vacuolar membrane.

ATP6V1H

GO:0000226

BP

microtubule cytoskeleton organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.

EML1, MID1, DYNC1LI2, OBSL1, ZPR1, VAMP4, TACC1, TACC2, PCNT, GAPDH, CDK1, CNP, MAPT, MAP2, NEFH, SON, TUBG1, WEE1, ATXN3, TUBA1B, MAP1A, PTK2, CAMSAP2, MAP7, CUL7, MAP7D1, PHLDB2, GAS2L3, TTL, ULK4, MARK4, DOCK7, CCDC8, EML4, RNF19A, MARK1, CAMSAP3, UXT, TACC3

GO:0000228

CC

nuclear chromosome

A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.

BIRC5, H2AFY, SMC2, ZBED1, JUN, TOP1, TOP2A, MSH3, MSH6, HMGA2, BLM, HIST1H4A, HIST1H3D, H3F3A, EXOSC9, RAD51, SPIDR, NCAPD2, SETX, PBRM1, HDAC8

GO:0000235

CC

astral microtubule

Any of the spindle microtubules that radiate in all directions from the spindle poles and are thought to contribute to the forces that separate the poles and position them in relation to the rest of the cell.

MAP9, KIF18B

GO:0000242

CC

pericentriolar material

A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome.

CEP152, TNKS, TCP1, TUBG1, PCM1, HOOK3, NIN, NEK1, TNKS2, TUBE1

GO:0000243

CC

commitment complex

A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript.

SNRPC, SNRPD1, SNRPD3, SNRNP35, PRPF39