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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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:0000244

BP

spliceosomal tri-snRNP complex assembly

The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.

PRPF3, SRSF10, CD2BP2, SART3, PRPF31, DDX20, PRPF19

GO:0000245

BP

spliceosomal complex assembly

The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.

GCFC2, RBM5, SNRPD1, SNRPD2, SNRPD3, SRPK2, SART3, GEMIN6, SCAF11, CRNKL1, PRPF19, LSM4

GO:0000255

BP

allantoin metabolic process

The chemical reactions and pathways involving allantoin, (2,5-dioxo-4-imidazolidinyl)urea, an intermediate or end product of purine catabolism.

GHR, STAT5A, STAT5B

GO:0000266

BP

mitochondrial fission

The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.

PARK2, OPA1, MTFR1, MTFR2, MFF

GO:0000271

BP

polysaccharide biosynthetic process

The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

NDST1, GLT8D1

GO:0000272

BP

polysaccharide catabolic process

The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

CHIT1

GO:0000278

BP

mitotic cell cycle

Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.

RRM1, CDC25B, CENPF, NEK4, CDH13, CENPE, CENPC, PAK2, FAM175B, CENPW, KIF18B, CDC5L, AZI2, NUDT15, STK24

GO:0000281

BP

mitotic cytokinesis

A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.

KIF20A, KIF4A, STAMBP, STMN1, SON, RASA1, APC, CENPA, PLK1, SPTBN1, KIF23, ANK3, CUL7, CEP55, SNX33, MITD1, CKAP2, SNX18, NUSAP1, RACGAP1, CHMP4B, ANLN, SPAST, SNX9

GO:0000288

BP

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.

POLR2D, CNOT3, ZFP36, ZFP36L2, ZFP36L1

GO:0000289

BP

nuclear-transcribed mRNA poly(A) tail shortening

Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.

CNOT1, CNOT3, PARN, CNOT4, EIF4E, EIF4B, ZFP36, MLH1, EIF4A1, EIF4A2, PAN3, SAMD4B, PAIP1, CNOT7, CNOT6, SAMD4A

GO:0000290

BP

deadenylation-dependent decapping of nuclear-transcribed mRNA

Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.

PAN3, DCP2, CNOT7, NOCT

GO:0000291

BP

nuclear-transcribed mRNA catabolic process, exonucleolytic

The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail.

POLR2G

GO:0000301

BP

retrograde transport, vesicle recycling within Golgi

The retrograde movement of substances within the Golgi, mediated by COP I vesicles. Cis-Golgi vesicles are constantly moving forward through the Golgi stack by cisternal progression, eventually becoming trans-Golgi vesicles. They then selectively transport membrane and luminal proteins from the trans- to the medial-Golgi while leaving others behind in the trans-Golgi cisternae; similarly, they selectively move proteins from the medial- to the cis-Golgi.

CUX1

GO:0000302

BP

response to reactive oxygen species

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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.

CCS, GSR, APOE, SOD2, CYBB, APOD, GPX1, P4HB, SOD3, GSTP1, TXN, GPX3, PRDX6, S100A7, PRDX2, CYCS, PRDX1, HYAL2, TXNRD1, GPX8, ERO1A, NOX5, GPX7, TXN2, NOX4, PPARGC1A

GO:0000303

BP

response to superoxide

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 superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.

SOD2, UCP2, UCP3

GO:0000320

BP

re-entry into mitotic cell cycle

The resumption of the mitotic cell division cycle by cells that were in a quiescent or other non-dividing state.

CCNF, GSK3B

GO:0000338

BP

protein deneddylation

The removal of a ubiquitin-like protein of the NEDD8 type from a protein.

TOR1A

GO:0000350

BP

generation of catalytic spliceosome for second transesterification step

Conformational rearrangement of the spliceosomal complex containing the RNA products from the 1st step of splicing to form the catalytic site for the second step of splicing.

PRPF18

GO:0000354

BP

cis assembly of pre-catalytic spliceosome

Assembly of a spliceosomal complex containing the intact pre-mRNA and all of the spliceosomal snRNPs. This occurs when the tri-snRNP associates with the pre-mRNA and associated snRNPs in an ATP-dependent manner.

DDX23

GO:0000375

BP

RNA splicing, via transesterification reactions

Splicing of RNA via a series of two transesterification reactions.

PRPF3, SRSF10, TRA2B, SF3A3, SRRM1, KHSRP, SNRNP40, SCAF11, DDX23

GO:0000380

BP

alternative mRNA splicing, via spliceosome

The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition.

KDM1A, PQBP1, SFPQ, PTBP1, HNRNPM, SRSF1, SRSF6, CDK13, RBM17, RSRC1, ESRP2

GO:0000381

BP

regulation of alternative mRNA splicing, via spliceosome

Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.

SAP18, RBFOX2, HNRNPL, DDX5, PTBP1, RBMX, RBM25, RBM5, TRA2B, SRSF2, FMR1, SRSF6, WTAP, RNPS1, MBNL2, UHMK1, SREK1, RBM4, RBFOX1, THRAP3, RBM8A

GO:0000387

BP

spliceosomal snRNP assembly

The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.

SNRPC, SNRPB, GEMIN4, SNRPF, SNRPD1, SNRPD2, SNRPD3, SART3, GEMIN5, GEMIN6, RBM22, GEMIN8, DDX20, LSM4

GO:0000389

BP

mRNA 3'-splice site recognition

Recognition of the intron 3'-splice site by components of the assembling U2- or U12-type spliceosome.

SF3A3

GO:0000395

BP

mRNA 5'-splice site recognition

Recognition of the intron 5'-splice site by components of the assembling spliceosome.

PSIP1, SNRPC, SRSF1, PRPF39

GO:0000398

BP

mRNA splicing, via spliceosome

The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.

DDX39A, POLR2D, DHX15, HNRNPR, PRPF3, PPIH, PLRG1, NUDT21, DHX16, SYNCRIP, PRPF40A, SRSF10, CD2BP2, LSM8, HNRNPC, SNRPA, SNRPC, HNRNPA1, SNRPA1, GTF2F2, SNRPB, HNRNPL, DDX5, POLR2E, HNRNPA2B1, POLR2A, PTBP1, POLR2B, HNRNPH3, HNRNPH1, GTF2F1, FUS, POLR2I, RBMX, BUD31, SKIV2L2, PAPOLA, NOVA1, HNRNPA3, HNRNPM, POLR2J, RBM5, POLR2K, SNU13, HNRNPH2, SNRPF, LSM3, LSM6, SNRPD1, SNRPD2, SNRPD3, POLR2G, POLR2L, TRA2B, SNRPN, YBX1, HNRNPU, SRSF2, SRSF11, SRSF1, NCBP1, CPSF1, SF3A3, CSTF3, SRSF9, SRSF5, SRSF6, PRPF4B, TRA2A, HNRNPD, SART3, NONO, RNPS1, PCBP1, ELAVL1, SNRNP35, FIP1L1, CWC27, DDX46, DHX32, PABPN1, ALYREF, CCAR1, SRRM1, ZCRB1, GEMIN5, SNRNP27, PRPF31, GEMIN6, PSPC1, RBPMS, SNRNP40, RSRC1, RNPC3, ZMAT2, RBM15, SPEN, CDC5L, BUD13, HNRNPUL1, DDX23, SNRNP25, SF3B5, CRNKL1, PNN, DHX35, METTL14, CWC22, RAVER2, RBM22, CWC15, CPSF2, LSM7, PRPF19, PPIE, NOVA2, SRRM2, LSM2, RBMX2, SF3B6, LSM5, LSM4, RBM8A

GO:0000413

BP

protein peptidyl-prolyl isomerization

The modification of a protein by cis-trans isomerization of a proline residue.

PPIH, PPIB, FKBP2, PPIF, NKTR, PPIC, RANBP2, PPIA, FKBP3, FKBP4, PPID, PPIL2, PPIG, FKBP5, PPP2R4, CWC27, PPIL4, FKBP10, FKBP14, FKBP11, PPIE, PIN4, FKBP7

GO:0000422

BP

mitophagy

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

PARK2, ATG12, GABARAPL2, BNIP3, SQSTM1, WIPI1, CISD2, RB1CC1, ATG2B, FUNDC2, PINK1, GABARAPL1, MAP1LC3A, PPARGC1A, WDR45, WIPI2

GO:0000430

BP

regulation of transcription from RNA polymerase II promoter by glucose

Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.

USF2

GO:0000432

BP

positive regulation of transcription from RNA polymerase II promoter by glucose

Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter.

USF2

GO:0000435

BP

positive regulation of transcription from RNA polymerase II promoter by galactose

Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter.

NCOA1

GO:0000447

BP

endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.

UTP20, RPSA, RPS21, RRS1, RCL1, FCF1

GO:0000448

BP

cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Endonucleolytic cleavage within ITS2 between the 5.8S rRNA and the LSU-rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.

BOP1

GO:0000453

BP

enzyme-directed rRNA 2'-O-methylation

The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA.

MRM1

GO:0000454

BP

snoRNA guided rRNA pseudouridine synthesis

The intramolecular conversion of uridine to pseudouridine in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of pseudouridylation.

NOP10, GAR1

GO:0000460

BP

maturation of 5.8S rRNA

Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule.

NSA2, SKIV2L2, EIF6, C1D, EXOSC4, WDR37, LAS1L

GO:0000461

BP

endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Endonucleolytic cleavage at the 3'-end of the SSU-rRNA from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.

RPSA, RPS21

GO:0000462

BP

maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.

UTP20, RPS8, RPS16, RPS14, TBL3, TSR1, NGDN, EMG1, UTP23, DCAF13, CCDC59, WDR3, FCF1, UTP18

GO:0000463

BP

maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.

RPL7, RPL35, BOP1, WDR12

GO:0000466

BP

maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Any process involved in the maturation of an rRNA molecule originally produced as part of a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.

WDR12

GO:0000467

BP

exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.

ERI2, ERI3, EXOSC9, EXOSC2, EXOSC7, EXOSC8, EXOSC3

GO:0000469

BP

cleavage involved in rRNA processing

Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule.

NOB1

GO:0000470

BP

maturation of LSU-rRNA

Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.

RSL1D1, NSA2, NOP2, SNU13, EIF6, RPL7A, RPL10A, MRPL1, WDR37, LAS1L

GO:0000472

BP

endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.

UTP20

GO:0000478

BP

endonucleolytic cleavage involved in rRNA processing

Any endonucleolytic cleavage involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. Some endonucleolytic cleavages produce the mature end, while others are a step in the process of generating the mature end from the pre-rRNA.

LAS1L

GO:0000479

BP

endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with three genes, in this order, are produced in the nuclei of many eukaryotic species, including S. cerevisiae.

TSR1

GO:0000480

BP

endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Endonucleolytic cleavage within the 5'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. Endonucleolytic cleavage within the 5'-ETS of the pre-RNA is conserved as one of the early steps of rRNA processing in all eukaryotes, but the specific position of cleavage is variable.

UTP20, UTP23, RCL1, FCF1

GO:0000492

BP

box C/D snoRNP assembly

The aggregation, arrangement and bonding together of proteins and a box C/D snoRNA to form a box C/D small nucleolar ribonucleoprotein (snoRNP) complex.

NUFIP1, RUVBL2, RUVBL1

GO:0000495

BP

box H/ACA snoRNA 3'-end processing

Any process involved in forming the mature 3' end of a box H/ACA snoRNA molecule.

DKC1

GO:0000578

BP

embryonic axis specification

The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo.

COBL, CTNNB1, STIL, CITED1

GO:0000707

BP

meiotic DNA recombinase assembly

During meiosis, the aggregation, arrangement and bonding together of strand exchange proteins (recombinases) to form higher order oligomers on single-stranded DNA.

RAD51D