Please use this identifier to cite or link to this item:
標題: 以乳癌為例-全面性探討蛋白質轉譯後修飾作用之間的交互作用
Using Bioinformatics Methods to Identify PTMs Crosstalk: An Example of Breast Cancer
作者: Chian-Ying Chen
關鍵字: Post-Translational Modification;Interaction (Crosstalk);Breast Cancer;蛋白質轉譯後修飾;交互作用;乳癌
引用: Alves G, Tatro A, Fanning T (1996) Differential methylation of human LINE-1 retrotransposons in malignant cells. Gene 176: 39-44 Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S (2004) Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4: 1633-1649 Brunak RGaS (2002) Prediction of glycosylation across the human proteome and the correlation to protein function. Pacific Symposium on Biocomputing Butt AM, Feng D, Idrees M, Tong Y, Lu J (2012a) Computational Identification and Modeling of Crosstalk between Phosphorylation, O-beta-glycosylation and Methylation of FoxO3 and Implications for Cancer Therapeutics. International journal of molecular sciences 13: 2918-2938 Butt AM, Feng D, Nasrullah I, Tahir S, Idrees M, Tong Y, Lu J (2012b) Computational identification of interplay between phosphorylation and O-beta-glycosylation of human occludin as potential mechanism to impair hepatitis C virus entry. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 12: 1235-1245 Chauhan JS, Rao A, Raghava GPS (2013) In silico Platform for Prediction of N-, O- and C-Glycosites in Eukaryotic Protein Sequences. PLoS ONE 8: e67008 Cuenca AG, Delano MJ, Kelly-Scumpia KM, Moreno C, Scumpia PO, Laface DM, Heyworth PG, Efron PA, Moldawer LL (2011) A paradoxical role for myeloid-derived suppressor cells in sepsis and trauma. Molecular medicine (Cambridge, Mass) 17: 281-292 Daniels MA, Hogquist KA, Jameson SC (2002) Sweet 'n' sour: the impact of differential glycosylation on T cell responses. Nature immunology 3: 903-910 de Queiroz RM, Carvalho E, Dias WB (2014) O-GlcNAcylation: The Sweet Side of the Cancer. Frontiers in oncology 4: 132 Douglas Hanahan1 RAW (2000) The Hallmarks of Cancer. Cell 100 Dwek MV, Ross HA, Leathem AJ (2001) Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer. Proteomics 1: 756-762 Esteve PO, Chang Y, Samaranayake M, Upadhyay AK, Horton JR, Feehery GR, Cheng X, Pradhan S (2011) A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nature structural & molecular biology 18: 42-48 Fernandes MR, de Carvalho DC, dos Santos AK, dos Santos SE, de Assumpcao PP, Burbano RM, dos Santos NP (2013) Association of slow acetylation profile of NAT2 with breast and gastric cancer risk in Brazil. Anticancer research 33: 3683-3689 Hart GW, Slawson C, Ramirez-Correa G, Lagerlof O (2011) Crosstalk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease. Annual review of biochemistry 80: 825-858 Hochgrafe F, Zhang L, O'Toole SA, Browne BC, Pinese M, Porta Cubas A, Lehrbach GM, Croucher DR, Rickwood D, Boulghourjian A, Shearer R, Nair R, Swarbrick A, Faratian D, Mullen P, Harrison DJ, Biankin AV, Sutherland RL, Raftery MJ, Daly RJ (2010) Tyrosine phosphorylation profiling reveals the signaling network characteristics of Basal breast cancer cells. Cancer research 70: 9391-9401 Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic acids research 40: D261-270 Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids research 40: D306-312 Jayashree Mohandass SR, Koganti Srilakshmi, Chinnasamy Perumal Rajadurai, Sangeetha Sanmugasamy, Gopal Ramesh Kumar (2010) BCDB - A database for breast cancer research and information. Bioinformation 5 Jiang W, Zhang Y, Meng F, Lian B, Chen X, Yu X, Dai E, Wang S, Liu X, Li X, Wang L, Li X (2013) Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease. Bioinformatics 29: 2596-2602 Kiemer L, Bendtsen JD, Blom N (2005) NetAcet: prediction of N-terminal acetylation sites. Bioinformatics 21: 1269-1270 Lee JSaK-J (2003) Post-translational Modifications and Their Biological Functions-proteomic analysis and systematic approaches. Journal of Biochemistry and Molecular Biology 37 McLarty JL, Marsh SA, Chatham JC (2013) Post-translational protein modification by O-linked N-acetyl-glucosamine: its role in mediating the adverse effects of diabetes on the heart. Life sciences 92: 621-627 Minguez P, Letunic I, Parca L, Bork P (2013) PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic acids research 41: D306-311 Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P (2012) Deciphering a global network of functionally associated post-translational modifications. Molecular systems biology 8: 599 Mosca R, Ceol A, Stein A, Olivella R, Aloy P (2014) 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic acids research 42: D374-379 Munster PN, Troso-Sandoval T, Rosen N, Rifkind R, Marks PA, Richon VM (2001) The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells. Cancer research 61: 8492-8497 Nikolaj Blom SG, S?ren Brunak (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular Biology 294 Peng M, Scholten A, Heck AJ, van Breukelen B (2013) Identification of Enriched PTM Crosstalk Motifs from Large-Scale Experimental Data Sets. Journal of proteome research Raghavachari B, Tasneem A, Przytycka TM, Jothi R (2008) DOMINE: a database of protein domain interactions. Nucleic acids research 36: D656-661 Rao RSP, Xu D, Thelen JJ, Miernyk JA (2013) Circles within circles crosstalk between protein Ser Thr Tyr phosphorylation and Met oxidation. Bioinformatics 14 Rudeina A Baasiri SRG, David L Ste?en and David A Wheeler (1999) The Breast cancer Gene Database-a collaborative information resource. Oncogene 18 S-I Hayashi HE, K Tanimoto, T Yoshida, Y Omoto, A Inoue,, Yamaguchi NYaY (2003) The expression and function of estrogen receptor alpha and beta in human breast cancer and its clinical application. Endocrine-related cancer 10 Schwartz D, Gygi SP (2005) An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nature biotechnology 23: 1391-1398 Shi S-P, Qiu J-D, Sun X-Y, Suo S-B, Huang S-Y, Liang R-P (2012) PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme. PLoS ONE 7: e38772 Slawson C, Hart GW (2011) O-GlcNAc signalling: implications for cancer cell biology. Nature reviews Cancer 11: 678-684 Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H (2013) Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. The EMBO journal 32: 1478-1488 Tang H, Goldberg E (2009) Homo sapiens lactate dehydrogenase c (Ldhc) gene expression in cancer cells is regulated by transcription factor Sp1, CREB, and CpG island methylation. Journal of andrology 30: 157-167 Ulrich Omasits CHA, Sebastian M?ller, Bernd Wollscheid (2013) Protter-interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics Venne AS, Kollipara L, Zahedi RP (2014) The next level of complexity: crosstalk of posttranslational modifications. Proteomics 14: 513-524 Yan L, Yang X, Davidson N (2001) Role of DNA Methylation and Histone Acetylation in Steroid Receptor Expression in Breast Cancer. J Mammary Gland Biol Neoplasia 6: 183-192 Zhike Lu ZC, Yingming Zhao, Samuel L. Volchenboum (2011) Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation. PLoS ONE 6
Post-Translational Modifications (PTMs) of proteins have the significant associations with regulating cell physiological function, gene regulation, protein function, generation of major diseases. However, most of the current studies only explore for the single protein-translational modification, two or more post-translational modifications of proteins between the role relevant information on their interaction still very few.
As a result, in this study of breast cancer for example. According to the methods of bioinformatics, after collecting a large number of breast cancer associated proteins and verified post-translational modifications data, motif and domain related information. In this study, we obtain the post-translational sites between two or more interaction of post-translational modifications after the statistical tests and functional analysis of species conservation, and the analysis of sequence, motif and domain, and the results of the protein-protein, domain-domain interaction network related tools DOMINE, 3did and PTMcode.
In addition to investigate the correlation between the interactions of post-translational modifications, this study will supply the biological laboratories to do extended discussion with further regulatory pathway of biological and physiological functions related diseases.

其他識別: U0005-2811201416195151
Rights: 同意授權瀏覽/列印電子全文服務,2014-08-31起公開。
Appears in Collections:基因體暨生物資訊學研究所

Files in This Item:
File SizeFormat Existing users please Login
nchu-103-7101019003-1.pdf10.29 MBAdobe PDFThis file is only available in the university internal network    Request a copy
Show full item record

Google ScholarTM


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.