{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T19:35:39Z","timestamp":1762544139592,"version":"3.40.3"},"publisher-location":"Cham","reference-count":33,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030453848"},{"type":"electronic","value":"9783030453855"}],"license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-3-030-45385-5_23","type":"book-chapter","created":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T12:13:38Z","timestamp":1590581618000},"page":"249-260","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Topological Analysis of Cancer Protein Subnetwork in Deubiquitinase (DUB) Interactome"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3235-8691","authenticated-orcid":false,"given":"Nurulisa","family":"Zulkifle","sequence":"first","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,4,30]]},"reference":[{"issue":"6","key":"23_CR1","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","volume":"122","author":"U Stelzl","year":"2005","unstructured":"Stelzl, U., et al.: A human protein-protein interaction network: a resource for annotating the proteome. Cell 122(6), 957\u2013968 (2005)","journal-title":"Cell"},{"issue":"4","key":"23_CR2","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.sbi.2005.06.001","volume":"15","author":"DP Ryan","year":"2005","unstructured":"Ryan, D.P., Matthews, J.M.: Protein-protein interactions in human disease. Curr. Opin. Struct. Biol. 15(4), 441\u2013446 (2005)","journal-title":"Curr. Opin. Struct. Biol."},{"issue":"12","key":"23_CR3","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.17576\/jsm-2018-4712-01","volume":"47","author":"S Harun","year":"2018","unstructured":"Harun, S., Zulkifle, N.: Construction and analysis of protein-protein interaction network to identify the molecular mechanism in laryngeal cancer. Sains Malays. 47(12), 2933\u20132940 (2018)","journal-title":"Sains Malays."},{"issue":"SP2","key":"23_CR4","first-page":"18","volume":"15","author":"N Zulkifle","year":"2019","unstructured":"Zulkifle, N., Che Rosli, A.F., Abdul Razak, S.R.: Bioinformatics analysis of differentially expressed genes in liver cancer for identification of key genes and pathways. Malaysian J. Med. Health Sci. 15(SP2), 18\u201324 (2019)","journal-title":"Malaysian J. Med. Health Sci."},{"issue":"3","key":"23_CR5","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/35056563","volume":"2","author":"AM Weissman","year":"2001","unstructured":"Weissman, A.M.: Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell Biol. 2(3), 169\u2013178 (2001)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"14","key":"23_CR6","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1096\/fasebj.11.14.9409543","volume":"11","author":"K Wilkinson","year":"1997","unstructured":"Wilkinson, K.: Regulation of ubiquitin dependent processes by deubiquitinating enzymes. FASEB J. 11(14), 1245\u20131256 (1997)","journal-title":"FASEB J."},{"issue":"8","key":"23_CR7","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1038\/nrm2731","volume":"10","author":"D Komander","year":"2009","unstructured":"Komander, D., et al.: Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10(8), 550\u2013563 (2009)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"23_CR8","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1146\/annurev.biochem.78.082307.091526","volume":"78","author":"FE Reyes-Turcu","year":"2009","unstructured":"Reyes-Turcu, F.E., et al.: Regulation and cellular roles of ubiquitin specific deubiquitinating enzymes. Annu. Rev. Biochem. 78, 363\u2013397 (2009)","journal-title":"Annu. Rev. Biochem."},{"issue":"5","key":"23_CR9","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1016\/j.cell.2005.11.007","volume":"123","author":"SNB Nijman","year":"2005","unstructured":"Nijman, S.N.B., et al.: A genomic and functional inventory of deubiquitinating enzymes. Cell 123(5), 773\u2013786 (2005)","journal-title":"Cell"},{"key":"23_CR10","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.molcel.2016.05.009","volume":"63","author":"SA Abdul Rehman","year":"2016","unstructured":"Abdul Rehman, S.A., et al.: MINDY 1 is a member of an evolutionarily conserved and structurally distinct new family of deubiquitinating enzymes. Mol. Cell 63, 146\u2013155 (2016)","journal-title":"Mol. Cell"},{"key":"23_CR11","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.molcel.2016.06.027","volume":"63","author":"T Maurer","year":"2016","unstructured":"Maurer, T., Wertz, I.E.: Length matters: MINDY is a new deubiquitinase family that preferentially cleaves long polyubiquitin chains. Mol. Cell 63, 4\u20136 (2016)","journal-title":"Mol. Cell"},{"issue":"6","key":"23_CR12","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1016\/j.cell.2013.05.014","volume":"153","author":"K Keusekkoten","year":"2013","unstructured":"Keusekkoten, K., et al.: OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1 linked polyubiquitin. Cell 153(6), 1312\u20131326 (2013)","journal-title":"Cell"},{"key":"23_CR13","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.molcel.2018.02.023","volume":"70","author":"D Kwasna","year":"2018","unstructured":"Kwasna, D., et al.: Discovery and characterization of ZUFSP\/ZUP1, a distinct deubiquitinase class important for genome stability. Mol. Cell 70, 150\u2013164 (2018)","journal-title":"Mol. Cell"},{"key":"23_CR14","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1016\/j.pharmthera.2017.03.001","volume":"177","author":"M He","year":"2017","unstructured":"He, M., et al.: Emerging role of DUBs in tumor metastasis and apoptosis: therapeutic implication. Pharmacol. Ther. 177, 96\u2013107 (2017)","journal-title":"Pharmacol. Ther."},{"issue":"11","key":"23_CR15","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon, P., et al.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11), 2498\u20132504 (2003)","journal-title":"Genome Res."},{"key":"23_CR16","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1007\/978-1-62703-450-0_4","volume":"1021","author":"PP Mill\u00e1n","year":"2013","unstructured":"Mill\u00e1n, P.P.: Visualization and analysis of biological networks. Methods Mol. Biol. 1021, 63\u201388 (2013)","journal-title":"Methods Mol. Biol."},{"issue":"Database issue","key":"23_CR17","doi-asserted-by":"publisher","first-page":"D561","DOI":"10.1093\/nar\/gkl958","volume":"35","author":"S Kerrien","year":"2007","unstructured":"Kerrien, S., et al.: IntAct\u2013open source resource for molecular interaction data. Nucleic Acids Res. 35(Database issue), D561\u2013D565 (2007)","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"23_CR18","doi-asserted-by":"publisher","first-page":"D572","DOI":"10.1093\/nar\/gkl950","volume":"35","author":"A Chatr-aryamontri","year":"2007","unstructured":"Chatr-aryamontri, A., et al.: MINT: the Molecular INTeraction database. Nucleic Acids Res. 35(Database issue), D572\u2013D574 (2007)","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"23_CR19","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nmeth.1931","volume":"9","author":"S Orchard","year":"2012","unstructured":"Orchard, S., et al.: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods 9(4), 345\u2013350 (2012)","journal-title":"Nat. Methods"},{"issue":"11","key":"23_CR20","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1038\/s41568-018-0060-1","volume":"18","author":"Z Sondka","year":"2018","unstructured":"Sondka, Z., et al.: The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat. Rev. Cancer 18(11), 696\u2013705 (2018)","journal-title":"Nat. Rev. Cancer"},{"issue":"D1","key":"23_CR21","doi-asserted-by":"publisher","first-page":"D940","DOI":"10.1093\/nar\/gkw1013","volume":"45","author":"WH Chen","year":"2017","unstructured":"Chen, W.H., et al.: OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Res. 45(D1), D940\u2013D944 (2017)","journal-title":"Nucleic Acids Res."},{"issue":"2","key":"23_CR22","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1093\/bioinformatics\/btm554","volume":"24","author":"Y Assenov","year":"2007","unstructured":"Assenov, Y., et al.: Computing topological parameters of biological networks. Bioinformatics 24(2), 282\u2013284 (2007)","journal-title":"Bioinformatics"},{"issue":"21","key":"23_CR23","doi-asserted-by":"publisher","first-page":"2857","DOI":"10.1093\/bioinformatics\/btp517","volume":"25","author":"G Scardoni","year":"2009","unstructured":"Scardoni, G., et al.: Analyzing biological network parameters with CentiScaPe. Bioinformatics 25(21), 2857\u20132859 (2009)","journal-title":"Bioinformatics"},{"key":"23_CR24","doi-asserted-by":"publisher","first-page":"2524","DOI":"10.12688\/f1000research.9203.2","volume":"5","author":"G Tosadori","year":"2017","unstructured":"Tosadori, G., et al.: Creating, generating and comparing random network models with NetworkRandomizer [version 3]. F1000Res. 5, 2524 (2017)","journal-title":"F1000Res."},{"key":"23_CR25","doi-asserted-by":"crossref","unstructured":"Zulkifle, N., Zulkifli, N.W.: Understanding human deubiquitinases target specificity by network based analysis towards their development as therapeutics target. In: Proceedings of the 9th International Conference on Computational Systems Biology and Bioinformatics (CSBio 2018), pp. 1\u20135. ACM, New York (2018)","DOI":"10.1145\/3291757.3291768"},{"key":"23_CR26","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1016\/j.cell.2011.02.016","volume":"144","author":"M Vidal","year":"2011","unstructured":"Vidal, M., et al.: Interactome networks and human disease. Cell 144, 986\u2013998 (2011)","journal-title":"Cell"},{"issue":"1","key":"23_CR27","doi-asserted-by":"publisher","first-page":"35","DOI":"10.2307\/3033543","volume":"40","author":"LC Freeman","year":"1977","unstructured":"Freeman, L.C.: A set of measures of centrality based on betweenness. Sociometry 40(1), 35\u201341 (1977)","journal-title":"Sociometry"},{"key":"23_CR28","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1002\/bs.3830100205","volume":"10","author":"MA Beauchamp","year":"1965","unstructured":"Beauchamp, M.A.: An improved index of centrality. Behav. Sci. 10, 161\u2013163 (1965)","journal-title":"Behav. Sci."},{"issue":"1","key":"23_CR29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3923\/ijbc.2013.1.14","volume":"7","author":"N Zulkifle","year":"2013","unstructured":"Zulkifle, N.: Systematic yeast two hybrid analysis of human E2 ubiquitin conjugating enzyme and deubiquitin (DUB) protein interactions. Int. J. Biol. Chem. 7(1), 1\u201314 (2013)","journal-title":"Int. J. Biol. Chem."},{"issue":"3","key":"23_CR30","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1016\/j.molcel.2012.01.011","volume":"45","author":"YC Juang","year":"2012","unstructured":"Juang, Y.C., et al.: OTUB1 co-opts Lys48 linked ubiquitin recognition to suppress E2 enzyme function. Mol. Cell 45(3), 384\u2013397 (2012)","journal-title":"Mol. Cell"},{"issue":"1","key":"23_CR31","doi-asserted-by":"publisher","first-page":"R1","DOI":"10.1530\/ERC-18-0264","volume":"26","author":"M Saldana","year":"2019","unstructured":"Saldana, M., et al.: Otubain 1: a non-canonical deubiquitinase with an emerging role in cancer. Endocr. Relat. Cancer 26(1), R1\u2013R14 (2019)","journal-title":"Endocr. Relat. Cancer"},{"key":"23_CR32","doi-asserted-by":"publisher","first-page":"135","DOI":"10.3389\/fphar.2018.00135","volume":"9","author":"L Guohong","year":"2018","unstructured":"Guohong, L., et al.: Jab1\/COPS5 as a novel biomarker for diagnosis, prognosis, therapy prediction and therapeutic tools for human cancer. Front. Pharmacol. 9, 135 (2018)","journal-title":"Front. Pharmacol."},{"key":"23_CR33","doi-asserted-by":"publisher","first-page":"427","DOI":"10.3389\/fphar.2019.00427","volume":"10","author":"Z Wang","year":"2019","unstructured":"Wang, Z., et al.: USP7: novel drug target in cancer therapy. Front. Pharmacol. 10, 427 (2019)","journal-title":"Front. Pharmacol."}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Biomedical Engineering"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-45385-5_23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T12:14:54Z","timestamp":1590581694000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-45385-5_23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"ISBN":["9783030453848","9783030453855"],"references-count":33,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-45385-5_23","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2020]]},"assertion":[{"value":"30 April 2020","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"IWBBIO","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Work-Conference on Bioinformatics and Biomedical Engineering","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Granada","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2020","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6 May 2020","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8 May 2020","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"iwbbio2020","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/iwbbio.ugr.es\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}