Construction of human activity-based phosphorylation networks

Molecular Systems Biology

Volumn 9, Issue , 2013, Pages

  Newman, Robert H ^a,b   Hu, Jianfei ^a   Rho, Hee Sool ^a   Xie, Zhi ^a   Woodard, Crystal ^a   Neiswinger, John ^a   Cooper, Christopher ^a   Shirley, Matthew ^a   Clark, Hillary M ^a   Hu, Shaohui ^a   Hwang, Woochang ^a   Seop Jeong, Jun ^a   Wu, George ^c   Lin, Jimmy ^d   Gao, Xinxin ^a   Ni, Qiang ^a   Goel, Renu ^e   Xia, Shuli ^f   Ji, Hongkai ^c   Dalby, Kevin N ^g   Birnbaum, Morris J ^h   Cole, Philip A ^a   Knapp, Stefan ⁱ   Ryazanov, Alexey G ^j   Zack, Donald J ^a   Blackshaw, Seth ^a,f   Pawson, Tony ^k,l   Gingras, Anne Claude ^k,l   Desiderio, Stephen ^a   Pandey, Akhilesh ^a   Turk, Benjamin E ^m   Zhang, Jin ^a,d   Zhu, Heng ^a,d   Qian, Jiang ^a,d   more..

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NORTH CAROLINA A AND T STATE UNIVERSITY   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^d JOHNS HOPKINS UNIVERSITY   (United States)

^e Institute of Bioinformatics   (India)

^f KENNEDY KRIEGER INSTITUTE   (United States)

^g UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^h UNIVERSITY OF PENNSYLVANIA   (United States)

ⁱ UNIVERSITY OF OXFORD   (United Kingdom)

^j UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY   (United States)

^k MOUNT SINAI HOSPITAL   (Canada)

^l UNIVERSITY OF TORONTO   (Canada)

^m YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

more..

Author keywords

phosphorylation; signaling networks; systems biology

Indexed keywords

BRUTON TYROSINE KINASE; CELL RECEPTOR; PROTEIN KINASE; B LYMPHOCYTE RECEPTOR; CYCLIC AMP DEPENDENT PROTEIN KINASE; PHOSPHOTRANSFERASE; AGAMMAGLOBULINAEMIA TYROSINE KINASE; LYMPHOCYTE ANTIGEN RECEPTOR; PROTEIN TYROSINE KINASE; TYROSINE;

ARTICLE; B LYMPHOCYTE; BIOINFORMATICS; CONSENSUS; HUMAN; HUMAN CELL; IN VIVO STUDY; INFORMATION; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; ENZYME SUBSTRATE; MASS SPECTROMETRY; SIGNAL TRANSDUCTION; ALGORITHM; AMINO ACID SEQUENCE; BAYES THEOREM; CYTOLOGY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION;

ALGORITHMS; AMINO ACID SEQUENCE; B-LYMPHOCYTES; BAYES THEOREM; CYCLIC AMP-DEPENDENT PROTEIN KINASES; HUMANS; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPS; PROTEIN-TYROSINE KINASES; RECEPTORS, ANTIGEN, B-CELL; SIGNAL TRANSDUCTION; TYROSINE;

EID: 84876557296     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2013.12     Document Type: Article

References (34)

1. Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M (2010) A global protein kinase and phosphatase interaction network in yeast. Science 328: 1043-1046
2. Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jodicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K et al (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res 40: D242-D251
3. Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, Holstege FC, Weissman JS, Keogh MC, KollerD,Shokat KM, Krogan NJ (2009) Functional organization of the S. cerevisiae phosphorylation network. Cell 136: 952-963
4. Gao M, Karin M (2005) Regulating the regulators: control of protein ubiquitination and ubiquitin-like modifications by extracellular stimuli. Mol Cell 19: 581-593 (Pubitemid 41219435)
5. Ha VL, Bharti S, Inoue H, Vass WC, Campa F, Nie Z, de Gramont A, Ward Y, Randazzo PA (2008) ASAP3 is a focal adhesion-associated Arf GAP that functions in cell migration and invasion. J Biol Chem 283: 14915-14926
6. Hu J, Rho HS, Newman RH, Hwang W, Neiswinger J, Zhu H, Zhang J, Qian J (2013) Global analysis of phosphorylation networks in humans. BBA Prot Proteom (in press)
7. Hu J, Wan J, Hackler Jr. L, Zack DJ, Qian J (2010) Computational analysis of tissue-specific gene networks: application to murine retinal functional studies. Bioinformatics 26: 2289-2297
8. Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho HS, Woodard C, Wang H, Jeong JS, Long S, He X, Wade H, Blackshaw S, Qian J, Zhu H (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139: 610-622
9. Hutti JE, Jarrell ET, Chang JD, Abbott DW, Storz P, Toker A, Cantley LC, Turk BE (2004) A rapid method for determining protein kinase phosphorylation specificity. Nat Methods 1: 27-29
10. Ismail SA, Vetter IR, Sot B, Wittinghofer A (2010) The structure of an Arf-ArfGAP complex reveals a Ca2\+ regulatory mechanism. Cell 141: 812-821
11. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-453 (Pubitemid 37296271)
12. Kawakami Y, Hartman SE, Kinoshita E, Suzuki H, Kitaura J, Yao L, Inagaki N, Franco A, Hata D, Maeda-Yamamoto M, Fukamachi H, Nagai H, Kawakami T (1999) Terreic acid, a quinone epoxide inhibitor of Bruton's tyrosine kinase. Proc Natl Acad Sci USA 96: 2227-2232 (Pubitemid 29117896)
13. Lin D, Ippolito GC, Zong RT, Bryant J, Koslovsky J, Tucker P (2007) Bright/ARID3A contributes to chromatin accessibility of the immunoglobulin heavy chain enhancer. Mol Cancer 6: 23
14. Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jorgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB et al (2007) Systematic discovery of in vivo phosphorylation networks. Cell 129: 1415-1426 (Pubitemid 46962092)
15. MathivananS,AhmedM,Ahn NG, AlexandreH,AmanchyR,Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Bjorling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE et al (2008) Human Proteinpedia enables sharing of human protein data. Nat Biotechnol 26: 164-167 (Pubitemid 351225942)
16. Miller ML, Jensen LJ, Diella F, Jorgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE et al (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 1: ra2
17. Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C et al (2010) Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal 3: ra12
18. Molina H, Horn DM, Tang N, Mathivanan S, Pandey A (2007) Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci USA 104: 2199-2204 (Pubitemid 46391375)
19. Ni Q, Ganesan A, Aye-Han NN, Gao X, Allen MD, Levchenko A, Zhang J (2011) Signaling diversity of PKA achieved via a Ca2 \+-cAMP-PKA oscillatory circuit. Nat Chem Biol 7: 34-40
20. Olsen JV, BlagoevB, GnadF, MacekB, KumarC,Mortensen P,Mann M (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635-648 (Pubitemid 44647421)
21. Pahl HL, Baeuerle PA (1996) Control of gene expression by proteolysis. Curr Opin Cell Biol 8: 340-347 (Pubitemid 26179213)
22. Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, NaK,Choi EY, Yan F, ZhangF, Zhang Y, Snyder M, ChengY,Chen R, Marko-Varga G, Deutsch EW, Kim H, Kwon JY, Aebersold R et al (2012) The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol 30: 221-223
23. PtacekJ,DevganG,MichaudG,ZhuH,ZhuX,FasoloJ,GuoH, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M et al (2005) Global analysis of protein phosphorylation in yeast. Nature 438: 679-684 (Pubitemid 41740579)
24. Rajaiya J, Hatfield M, Nixon JC, Rawlings DJ, Webb CF (2005) Bruton's tyrosine kinase regulates immunoglobulin promoter activation in association with the transcription factor Bright. Mol Cell Biol 25: 2073-2084 (Pubitemid 40354608)
25. Rajaiya J, Nixon JC, Ayers N, Desgranges ZP, Roy AL, Webb CF (2006) Induction of immunoglobulin heavy-chain transcription through the transcription factor Bright requires TFII-I. Mol Cell Biol 26: 4758-4768 (Pubitemid 43877590)
26. Sampson DA, Wang M, Matunis MJ (2001) The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification. J Biol Chem 276: 21664-21669
27. Van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA et al (2010) Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 143: 991-1004
28. Wang Y, Ding SJ, Wang W, Jacobs JM, Qian WJ, Moore RJ, Yang F, Camp 2nd DG, Smith RD, Klemke RL (2007) Profiling signaling polarity in chemotactic cells. Proc Natl Acad Sci USA 10 4 : 8328-8333 (Pubitemid 47175487)
29. Whitmarsh AJ, Davis RJ (2000) Regulation of transcription factor function by phosphorylation. Cell Mol Life Sci 57: 1172-1183 (Pubitemid 30663475)
30. Yang F, Stenoien DL, Strittmatter EF, Wang J, Ding L, Lipton MS, Monroe ME, Nicora CD, Gristenko MA, Tang K, Fang R, Adkins JN, Camp 2nd DG, Chen DJ, Smith RD (2006) Phosphoproteome profiling of human skin fibroblast cells in response to low-and high-dose irradiation. J Proteome Res 5: 1252-1260 (Pubitemid 43727805)
31. Zheng XM, Resnick RJ, Shalloway D (2000) A phosphotyrosine displacement mechanism for activation of Src by PTPalpha. EMBO J 19: 964-978 (Pubitemid 30119822)
32. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M (2001) Global analysis of protein activities using proteome chips. Science 293: 2101-210 5
33. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M (2000) Analysis of yeast protein kinases using protein chips. Nat Genet 26: 283-289
34. Zhu J, Liao G, Shan L, Zhang J, Chen MR, Hayward GS, Hayward SD, Desai P, Zhu H (2009) Protein array identification of substrates of the Epstein-Barr virus protein kinase BGLF4. J Virol 83: 5219-5231