Generic Transcription Pathway
De Andrade JP, Park JM, Gu VW, Woodfield GW, Kulak MV, Lorenzen AW, Wu VT, Van Dorin SE, Spanheimer PM, Weigel RJ. EGFR Is Regulated by TFAP2C in Luminal Breast Cancer and Is a Target for Vandetanib. Mol Cancer Ther. 2016 Mar;15(3):503–11. PMID: 26832794; PMCID: PMC4783288.; Park JM, Wu T, Cyr AR, Woodfield GW, De Andrade JP, Spanheimer PM, Li T, Sugg SL, Lal G, Domann FE, Zhang W, Weigel RJ. The role of Tcfap2c in tumorigenesis and cancer growth in an activated Neu model of mammary carcinogenesis. Oncogene. 2015 Dec 10;34(50):6105–14. PMID: 25772240; PMCID: PMC4573379.; Li Q, Pan H, Guan L, Su D, Ma X. CITED2 mutation links congenital heart defects to dysregulation of the cardiac gene VEGF and PITX2C expression. Biochemical and Biophysical Research Communications. 2012 Jul;423(4):895–9. doi: 10.1016/j.bbrc.2012.06.099.; Huang H, Woo AJ, Waldon Z, Schindler Y, Moran TB, Zhu HH, Feng GS, Steen H, Cantor AB. A Src family kinase-Shp2 axis controls RUNX1 activity in megakaryocyte and T-lymphocyte differentiation. Genes Dev. 2012 Jul 15;26(14):1587–601. PMID: 22759635; PMCID: PMC3404386.; Liu H, Tan BC, Tseng KH, Chuang CP, Yeh CW, Chen KD, Lee SC, Yung BY. Nucleophosmin acts as a novel AP2alpha-binding transcriptional corepressor during cell differentiation. EMBO Rep. 2007 Apr;8(4):394–400. PMID: 17318229; PMCID: PMC1852768.; Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet. 2006;7():29–59. doi: 10.1146/annurev.genom.7.080505.115623. PMID: 16719718.; Bray SJ. Notch signalling: a simple pathway becomes complex. Nature Reviews Molecular Cell Biology. 2006 Sep;7(9):678–89. doi: 10.1038/nrm2009.; Rosenfeld MG, Lunyak VV, Glass CK. Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. Genes Dev. 2006 Jun 01;20(11):1405–28. doi: 10.1101/gad.1424806. PMID: 16751179.; Louvi A, Artavanis-Tsakonas S. Notch signalling in vertebrate neural development. Nat Rev Neurosci. 2006 Feb;7(2):93–102. doi: 10.1038/nrn1847. PMID: 16429119.; Malik S, Roeder RG. Dynamic regulation of pol II transcription by the mammalian Mediator complex. Trends Biochem Sci. 2005 May;30(5):256–63. doi: 10.1016/j.tibs.2005.03.009. PMID: 15896744.; Blazek E, Mittler G, Meisterernst M. The mediator of RNA polymerase II. Chromosoma. 2005 Mar;113(8):399–408. doi: 10.1007/s00412-005-0329-5. PMID: 15690163.; Roeder RG. Transcriptional regulation and the role of diverse coactivators in animal cells. FEBS Lett. 2005 Feb 07;579(4):909–15. doi: 10.1016/j.febslet.2004.12.007. PMID: 15680973.; Conaway JW, Florens L, Sato S, Tomomori-Sato C, Parmely TJ, Yao T, Swanson SK, Banks CA, Washburn MP, Conaway RC. The mammalian Mediator complex. FEBS Lett. 2005 Feb 07;579(4):904–8. doi: 10.1016/j.febslet.2004.11.031. PMID: 15680972.; Bamforth SD, Bragança J, Farthing CR, Schneider JE, Broadbent C, Michell AC, Clarke K, Neubauer S, Norris D, Brown NA, Anderson RH, Bhattacharya S. Cited2 controls left-right patterning and heart development through a Nodal-Pitx2c pathway. Nat Genet. 2004 Nov;36(11):1189–96. doi: 10.1038/ng1446. PMID: 15475956.; Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell. 2004 Jun 04;14(5):553–7. doi: 10.1016/j.molcel.2004.05.011. PMID: 15175151.; Schweisguth F. Regulation of Notch Signaling Activity. Current Biology. 2004 Feb;14(3):R129–38. doi: 10.1016/j.cub.2004.01.023.; Kadonaga JT. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell. 2004 Jan 23;116(2):247–57. doi: 10.1016/s0092-8674(03)01078-x. PMID: 14744435.; Ruiz M, Pettaway C, Song R, Stoeltzing O, Ellis L, Bar-Eli M. Activator protein 2alpha inhibits tumorigenicity and represses vascular endothelial growth factor transcription in prostate cancer cells. Cancer Res. 2004 Jan 15;64(2):631–8. doi: 10.1158/0008-5472.can-03-2751. PMID: 14744778.; Barolo S, Posakony JW. Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling. Genes Dev. 2002 May 15;16(10):1167–81. doi: 10.1101/gad.976502. PMID: 12023297.; Justice NJ, Jan YN. Variations on the Notch pathway in neural development. Curr Opin Neurobiol. 2002 Feb;12(1):64–70. doi: 10.1016/s0959-4388(02)00291-x. PMID: 11861166.; Näär AM, Lemon BD, Tjian R. Transcriptional coactivator complexes. Annu Rev Biochem. 2001;70():475–501. doi: 10.1146/annurev.biochem.70.1.475. PMID: 11395415.; Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Näär AM, Erdjument-Bromage H, Tempst P, Freedman LP. Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature. 1999 Apr 29;398(6730):824–8. doi: 10.1038/19783. PMID: 10235266.; Wang D, Shin TH, Kudlow JE. Transcription factor AP-2 controls transcription of the human transforming growth factor-alpha gene. J Biol Chem. 1997 May 30;272(22):14244–50. doi: 10.1074/jbc.272.22.14244. PMID: 9162057.; Valdez BC, Perlaky L, Saijo Y, Henning D, Zhu C, Busch RK, Zhang WW, Busch H. A region of antisense RNA from human p120 cDNA with high homology to mouse p120 cDNA inhibits NIH 3T3 proliferation. Cancer Res. 1992 Oct 15;52(20):5681–6. PMID: 1394192.
Metabolites
Enzyme
| EC Number | name | full name | note |
|---|---|---|---|
| 1.-.-.- | |||
| 1.1.1.49 | glucose-6-phosphate dehydrogenase (NADP+) | D-glucose-6-phosphate:NADP+ 1-oxidoreductase | |
| 1.11.1.12 | phospholipid-hydroperoxide glutathione peroxidase | glutathione:lipid-hydroperoxide oxidoreductase | |
| 1.11.1.2 | NADPH peroxidase | NADPH:hydrogen-peroxide oxidoreductase | |
| 1.11.1.24 | thioredoxin-dependent peroxiredoxin | thioredoxin:hydroperoxide oxidoreductase | |
| 1.11.1.6 | catalase | hydrogen-peroxide:hydrogen-peroxide oxidoreductase | |
| 1.11.1.9 | glutathione peroxidase | glutathione:hydrogen-peroxide oxidoreductase | |
| 1.14.11.67 | [histone H3]-trimethyl-L-lysine4 demethylase | [histone H3]-N6,N6,N6-trimethyl-L-lysine4,2-oxoglutarate:oxygen oxidoreductase | |
| 1.15.1.1 | superoxide dismutase | superoxide:superoxide oxidoreductase | |
| 1.17.4.1 | ribonucleoside-diphosphate reductase | 2'-deoxyribonucleoside-5'-diphosphate:thioredoxin-disulfide 2'-oxidoreductase | |
| 1.3.1.70 | DELTA14-sterol reductase | 4,4-dimethyl-5alpha-cholesta-8,24-dien-3beta-ol:NADP+ DELTA14-oxidoreductase | |
| 1.6.5.5 | NADPH:quinone reductase | NADPH:quinone oxidoreductase | |
| 1.8.1.9 | thioredoxin-disulfide reductase | thioredoxin:NADP+ oxidoreductase | |
| 2.1.1.2 | guanidinoacetate N-methyltransferase | S-adenosyl-L-methionine:N-guanidinoacetate methyltransferase | |
| 2.1.1.319 | type I protein arginine methyltransferase | S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega-dimethyl-L-arginine-forming) | |
| 2.1.1.320 | type II protein arginine methyltransferase | S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega'-dimethyl-L-arginine-forming) | |
| 2.1.1.354 | [histone H3]-lysine4 N-trimethyltransferase | S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase | |
| 2.1.1.356 | [histone H3]-lysine27 N-trimethyltransferase | S-adenosyl-L-methionine:[histone H3]-L-lysine27 N6-methyltransferase | |
| 2.1.1.361 | [histone H4]-lysine20 N-methyltransferase | S-adenosyl-L-methionine:[histone H4]-L-lysine20 N6-methyltransferase | |
| 2.1.1.364 | [histone H3]-lysine4 N-methyltransferase | S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase | |
| 2.1.1.367 | [histone H3]-lysine9 N-methyltransferase | S-adenosyl-L-methionine:[histone H3]-L-lysine9 N6-methyltransferase | |
| 2.3.1.15 | glycerol-3-phosphate 1-O-acyltransferase | acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase | |
| 2.3.1.286 | protein acetyllysine N-acetyltransferase | [protein]-N6-acetyl-L-lysine:NAD+ N-acetyltransferase (NAD+-hydrolysing; 2''-O-acetyl-ADP-D-ribose-forming) | |
| 2.3.1.48 | histone acetyltransferase | acetyl-CoA:[protein]-L-lysine acetyltransferase | |
| 2.3.1.57 | diamine N-acetyltransferase | acetyl-CoA:alkane-alpha,omega-diamine N-acetyltransferase | |
| 2.3.2.23 | E2 ubiquitin-conjugating enzyme | S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine:[E2 ubiquitin-conjugating enzyme] ubiquitinyl transferase | |
| 2.3.2.24 | (E3-independent) E2 ubiquitin-conjugating enzyme | S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine:L-lysine ubiquitinyl transferase ([E3 ubiquitin transferase]-independent) | |
| 2.3.2.26 | HECT-type E3 ubiquitin transferase | [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming) | |
| 2.3.2.27 | RING-type E3 ubiquitin transferase | [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (isopeptide bond-forming; RING-type) | |
| 2.3.2.32 | cullin-RING-type E3 NEDD8 transferase | [E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-L-cysteine:[cullin] [NEDD8-protein] transferase (isopeptide bond-forming; RING-type) | |
| 2.3.2.36 | RING-type E3 ubiquitin transferase (cysteine targeting) | [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein] ubiquitin transferase (thioester bond-froming; RING-type) | |
| 2.4.2.12 | nicotinamide phosphoribosyltransferase | nicotinamide-D-ribonucleotide:diphosphate phospho-alpha-D-ribosyltransferase | |
| 2.4.2.30 | NAD+ ADP-ribosyltransferase | NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase | |
| 2.5.1.60 | protein geranylgeranyltransferase type II | geranylgeranyl-diphosphate:protein-cysteine geranyltransferase | |
| 2.7.1.1 | hexokinase | ATP:D-hexose 6-phosphotransferase | |
| 2.7.1.149 | 1-phosphatidylinositol-5-phosphate 4-kinase | ATP:1-phosphatidyl-1D-myo-inositol-5-phosphate 4-phosphotransferase | |
| 2.7.10.1 | receptor protein-tyrosine kinase | ATP:[protein]-L-tyrosine O-phosphotransferase (receptor-type) | |
| 2.7.10.2 | non-specific protein-tyrosine kinase | ATP:[protein]-L-tyrosine O-phosphotransferase (non-specific) | |
| 2.7.11.1 | non-specific serine/threonine protein kinase | ATP:protein phosphotransferase (non-specific) | |
| 2.7.11.13 | protein kinase C | ATP:protein phosphotransferase (diacylglycerol-dependent) | |
| 2.7.11.17 | Ca2+/calmodulin-dependent protein kinase | ATP:protein phosphotransferase (Ca2+/calmodulin-dependent) | |
| 2.7.11.21 | polo kinase | ATP:protein phosphotransferase (spindle-pole-dependent) | |
| 2.7.11.22 | cyclin-dependent kinase | ATP:cyclin phosphotransferase | |
| 2.7.11.23 | [RNA-polymerase]-subunit kinase | ATP:[DNA-directed RNA polymerase] phosphotransferase | |
| 2.7.11.24 | mitogen-activated protein kinase | ATP:protein phosphotransferase (MAPKK-activated) | |
| 2.7.11.26 | tau-protein kinase | ATP:[tau-protein] O-phosphotransferase | |
| 2.7.12.1 | dual-specificity kinase | ATP:protein phosphotransferase (Ser/Thr- and Tyr-phosphorylating) | |
| 2.7.12.2 | mitogen-activated protein kinase kinase | ATP:protein phosphotransferase (MAPKKK-activated) | |
| 3.1.3.16 | protein-serine/threonine phosphatase | protein-serine/threonine-phosphate phosphohydrolase | |
| 3.1.3.46 | fructose-2,6-bisphosphate 2-phosphatase | beta-D-fructose-2,6-bisphosphate 2-phosphohydrolase | |
| 3.1.3.48 | protein-tyrosine-phosphatase | protein-tyrosine-phosphate phosphohydrolase | |
| 3.1.3.67 | phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase | 1-phosphatidyl-1D-myo-inositol-3,4,5-trisphosphate 3-phosphohydrolase | |
| 3.1.3.78 | phosphatidylinositol-4,5-bisphosphate 4-phosphatase | 1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase | |
| 3.1.3.9 | glucose-6-phosphatase | D-glucose-6-phosphate phosphohydrolase | |
| 3.4.19.12 | ubiquitinyl hydrolase 1 | ||
| 3.4.21.75 | Furin | ||
| 3.4.22.36 | caspase-1 | ||
| 3.4.22.38 | cathepsin K | ||
| 3.4.22.55 | caspase-2 | ||
| 3.4.22.59 | caspase-6 | ||
| 3.4.22.63 | caspase-10 | ||
| 3.5.1.2 | glutaminase | L-glutamine amidohydrolase | |
| 3.5.1.98 | histone deacetylase | histone amidohydrolase | |
| 3.6.4.13 | RNA helicase | ||
| 3.6.5.2 | small monomeric GTPase | GTP phosphohydrolase (cell-regulating) | |
| 4.1.1.15 | glutamate decarboxylase | L-glutamate 1-carboxy-lyase (4-aminobutanoate-forming) | |
| 4.1.1.32 | phosphoenolpyruvate carboxykinase (GTP) | GTP:oxaloacetate carboxy-lyase (adding GTP; phosphoenolpyruvate-forming) | |
| 5.2.1.8 | peptidylprolyl isomerase | Peptidylproline cis-trans-isomerase | |
| 5.3.1.9 | glucose-6-phosphate isomerase | alpha-D-glucose-6-phosphate aldose-ketose-isomerase (configuration-inverting) | |
| 5.6.1.7 | chaperonin ATPase | ATP phosphohydrolase (polypeptide-unfolding) | |
| 5.6.2.3 | DNA 5'-3' helicase | DNA 5'-3' helicase (ATP-hydrolysing) | |
| 5.6.2.4 | DNA 3'-5' helicase | DNA 3'-5' helicase (ATP-hydrolysing) |
Proteins
| Protein ID | name | full name |
|---|