{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T23:11:55Z","timestamp":1723245115496},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,3]]},"DOI":"10.1186\/s12859-017-1525-z","type":"journal-article","created":{"date-parts":[[2017,3,22]],"date-time":"2017-03-22T06:24:20Z","timestamp":1490163860000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Comparison of tissue\/disease specific integrated networks using directed graphlet signatures"],"prefix":"10.1186","volume":"18","author":[{"given":"Arzu Burcak","family":"Sonmez","sequence":"first","affiliation":[]},{"given":"Tolga","family":"Can","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,3,22]]},"reference":[{"issue":"suppl 1","key":"1525_CR1","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","volume":"39","author":"EG Cerami","year":"2011","unstructured":"Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011; 39(suppl 1):D685\u2013D690.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"1525_CR2","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkj109","volume":"34","author":"C Stark","year":"2006","unstructured":"Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006; 34(suppl 1):D535\u2013D539.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"1525_CR3","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","volume":"37","author":"TS Keshava Prasad","year":"2009","unstructured":"Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, et al. Human Protein Reference Database -2009 update. Nucleic Acids Res. 2009; 37(suppl 1):D767\u2013D772.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"1525_CR4","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","volume":"28","author":"E Demir","year":"2010","unstructured":"Demir E, Cary M, Paley S, et al. BioPAX - A community standard for pathway data sharing. Nature biotechnol. 2010; 28(9):935\u2013942.","journal-title":"Nature biotechnol"},{"issue":"9","key":"1525_CR5","first-page":"1","volume":"09;9","author":"E Demir","year":"2013","unstructured":"Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, et al. Using Biological Pathway Data with Paxtools. PLoS Comput Biol. 2013; 09;9(9):1\u20135.","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"1525_CR6","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1093\/bioinformatics\/btv620","volume":"32","author":"T Will","year":"2016","unstructured":"Will T, Helms V. PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. Bioinformatics. 2016; 32(4):571\u2013578.","journal-title":"Bioinformatics"},{"issue":"D1","key":"1525_CR7","doi-asserted-by":"crossref","first-page":"D536\u2014D541","DOI":"10.1093\/nar\/gkv1115","volume":"44","author":"M Kotlyar","year":"2016","unstructured":"Kotlyar M, Pastrello C, Sheahan N, Jurisica I. Integrated interactions database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Res. 2016; 44(D1):D536\u2014D541.","journal-title":"Nucleic Acids Res"},{"key":"1525_CR8","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/ng.3259","volume":"47","author":"CS Greene","year":"2015","unstructured":"Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, et al. Understanding multicellular function and disease with human tissue-specific networks. Nature Gen. 2015; 47:569\u2013576.","journal-title":"Nature Gen"},{"issue":"20","key":"1525_CR9","doi-asserted-by":"crossref","first-page":"12380","DOI":"10.1093\/nar\/gku923","volume":"42","author":"S Zhang","year":"2014","unstructured":"Zhang S, Tian D, Tran NH, Choi KP, Zhang L. Profiling the transcription factor regulatory networks of human cell types. Nucleic Acids Res. 2014; 42(20):12380\u201312387.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"1525_CR10","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1093\/bioinformatics\/btu786","volume":"31","author":"CY Park","year":"2015","unstructured":"Park CY, Krishnan A, Zhu Q, Wong AK, Lee YS, Troyanskaya OG. Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics. 2015; 31(7):1093\u20131101.","journal-title":"Bioinformatics"},{"issue":"2","key":"1525_CR11","doi-asserted-by":"crossref","first-page":"e177\u2014e183","DOI":"10.1093\/bioinformatics\/btl301","volume":"23","author":"N Pr\u017eulj","year":"2007","unstructured":"Pr\u017eulj N. Biological network comparison using graphlet degree distribution. Bioinformatics. 2007; 23(2):e177\u2014e183.","journal-title":"Bioinformatics"},{"issue":"4","key":"1525_CR12","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1093\/bioinformatics\/bts729","volume":"29","author":"W Hayes","year":"2013","unstructured":"Hayes W, Sun K, Pr\u017eulj N. Graphlet-based measures are suitable for biological network comparison. Bioinformatics. 2013; 29(4):483\u2013491.","journal-title":"Bioinformatics"},{"issue":"2","key":"1525_CR13","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1016\/j.comnet.2011.08.019","volume":"56","author":"D Marcus","year":"2012","unstructured":"Marcus D, Shavitt Y. RAGE - A rapid graphlet enumerator for large networks. Computer Netw. 2012; 56(2):810\u2013819.","journal-title":"Computer Netw"},{"issue":"5","key":"1525_CR14","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1109\/TCBB.2014.2321150","volume":"11","author":"LAA Meira","year":"2014","unstructured":"Meira LAA, M\u00e1ximo VR, Fazenda AL, Da Concei\u00e7\u00e3o AF. Acc-Motif: Accelerated Network Motif Detection. IEEE\/ACM Trans Comput Biol Bioinformatics. 2014; 11(5):853\u2013862.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinformatics"},{"issue":"4","key":"1525_CR15","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1093\/bioinformatics\/btt717","volume":"30","author":"T Hocevar","year":"2014","unstructured":"Hocevar T, Dem\u0161ar J. A combinatorial approach to graphlet counting. Bioinformatics. 2014; 30(4):559\u2013565.","journal-title":"Bioinformatics"},{"issue":"1","key":"1525_CR16","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002; 30(1):207\u2013210.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"1525_CR17","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res. 2003; 13(11):2498\u20132504.","journal-title":"Genome Res"},{"key":"1525_CR18","unstructured":"The Pathway Commons Database Version 8; [cited April 21, 2016]. Available from: http:\/\/www.pathwaycommons.org\/archives\/PC2\/v8\/ ."},{"issue":"D1","key":"1525_CR19","first-page":"D1079\u2014D1085","volume":"43","author":"KA Gray","year":"2015","unstructured":"Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015; 43(D1):D1079\u2014D1085.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"1525_CR20","doi-asserted-by":"crossref","first-page":"D472","DOI":"10.1093\/nar\/gkt1102","volume":"42","author":"D Croft","year":"2014","unstructured":"Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014; 42(D1):D472\u2013D477.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1525_CR21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-11-1","volume":"11","author":"Y Li","year":"2010","unstructured":"Li Y, Liu L, Bai X, Cai H, Ji W, Guo D, et al. Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks. BMC Bioinforma. 2010; 11(1):1\u20136.","journal-title":"BMC Bioinforma"},{"key":"1525_CR22","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","volume":"34","author":"AI Saeed","year":"2003","unstructured":"Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003; 34:374\u2013378.","journal-title":"Biotechniques"},{"key":"1525_CR23","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DV Huang","year":"2008","unstructured":"Huang DV, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2008; 4:44\u201357.","journal-title":"Nat Protoc"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1525-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,19]],"date-time":"2019-09-19T22:16:23Z","timestamp":1568931383000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1525-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3]]},"references-count":23,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2017,3]]}},"alternative-id":["1525"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1525-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3]]},"article-number":"135"}}