{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T22:33:02Z","timestamp":1790548382540,"version":"4.1.0"},"reference-count":78,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:00:00Z","timestamp":1736380800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:00:00Z","timestamp":1736380800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100007586","name":"Aix-Marseille Universit\u00e9","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007586","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Charles University, Czech Republic"},{"DOI":"10.13039\/501100004410","name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004410","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["EJP RD COFUND-EJP N\u00b0 825575"],"award-info":[{"award-number":["EJP RD COFUND-EJP N\u00b0 825575"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["EJP RD COFUND-EJP N\u00b0 825575"],"award-info":[{"award-number":["EJP RD COFUND-EJP N\u00b0 825575"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["EJP RD COFUND-EJP N\u00b0 825575"],"award-info":[{"award-number":["EJP RD COFUND-EJP N\u00b0 825575"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["EJP RD COFUND-EJP N\u00b0 825575"],"award-info":[{"award-number":["EJP RD COFUND-EJP N\u00b0 825575"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["EJP RD COFUND-EJP N\u00b0 825575"],"award-info":[{"award-number":["EJP RD COFUND-EJP N\u00b0 825575"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["EJP RD COFUND-EJP N\u00b0 825575"],"award-info":[{"award-number":["EJP RD COFUND-EJP N\u00b0 825575"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-025-85580-4","type":"journal-article","created":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T06:51:04Z","timestamp":1736405464000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A collaborative network analysis for the interpretation of transcriptomics data in Huntington\u2019s disease"],"prefix":"10.1038","volume":"15","author":[{"given":"Ozan","family":"Ozisik","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nazli Sila","family":"Kara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tooba","family":"Abbassi-Daloii","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgane","family":"T\u00e9r\u00e9zol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa C.","family":"Kuijper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"N\u00faria","family":"Queralt-Rosinach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annika","family":"Jacobsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osman Ugur","family":"Sezerman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Roos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris T.","family":"Evelo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana\u00efs","family":"Baudot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Friederike","family":"Ehrhart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleni","family":"Mina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,1,9]]},"reference":[{"key":"85580_CR1","unstructured":"European Commission research and innovation on rare diseases. (2023). https:\/\/ec.europa.eu\/info\/research-and-innovation\/research-area\/health-research-and-innovation\/rare-diseases_en"},{"key":"85580_CR2","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1038\/s41431-019-0508-0","volume":"28","author":"S Nguengang Wakap","year":"2020","unstructured":"Nguengang Wakap, S. et al. Estimating cumulative point prevalence of rare diseases: Analysis of the Orphanet database. Eur. J. Hum. Genet. 28, 165\u2013173 (2020).","journal-title":"Eur. J. Hum. Genet."},{"key":"85580_CR3","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1186\/s13023-021-01923-0","volume":"16","author":"WA Gahl","year":"2021","unstructured":"Gahl, W. A. et al. Essential list of medicinal products for rare diseases: Recommendations from the IRDiRC Rare Disease Treatment Access Working Group. Orphanet J. Rare Dis. 16, 308 (2021).","journal-title":"Orphanet J. Rare Dis."},{"key":"85580_CR4","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/s41573-019-0049-9","volume":"19","author":"E Tambuyzer","year":"2020","unstructured":"Tambuyzer, E. et al. Therapies for rare diseases: Therapeutic modalities, progress and challenges ahead. Nat. Rev. Drug Discov. 19, 93\u2013111 (2020).","journal-title":"Nat. Rev. Drug Discov"},{"key":"85580_CR5","doi-asserted-by":"publisher","first-page":"W214","DOI":"10.1093\/nar\/gkq537","volume":"38","author":"D Warde-Farley","year":"2010","unstructured":"Warde-Farley, D. et al. The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 38, W214\u2013220 (2010).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR6","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","volume":"47","author":"D Szklarczyk","year":"2019","unstructured":"Szklarczyk, D. et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607\u2013D613 (2019).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR7","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, 2498\u20132504 (2003).","journal-title":"Genome Res."},{"key":"85580_CR8","doi-asserted-by":"publisher","first-page":"e1004085","DOI":"10.1371\/journal.pcbi.1004085","volume":"11","author":"M Kutmon","year":"2015","unstructured":"Kutmon, M. et al. PathVisio 3: An extendable pathway analysis toolbox. PLoS Comput. Biol. 11, e1004085 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"85580_CR9","doi-asserted-by":"publisher","first-page":"D613","DOI":"10.1093\/nar\/gkaa1024","volume":"49","author":"M Martens","year":"2021","unstructured":"Martens, M. et al. WikiPathways: Connecting communities. Nucleic Acids Res. 49, D613\u2013D621 (2021).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR10","doi-asserted-by":"publisher","first-page":"i451","DOI":"10.1093\/bioinformatics\/bts389","volume":"28","author":"E Glaab","year":"2012","unstructured":"Glaab, E., Baudot, A., Krasnogor, N., Schneider, R. & Valencia, A. EnrichNet: network-based gene set enrichment analysis. Bioinformatics 28, i451\u2013i457 (2012).","journal-title":"Bioinformatics"},{"key":"85580_CR11","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1038\/nrg3552","volume":"14","author":"K Mitra","year":"2013","unstructured":"Mitra, K., Carvunis, A. R., Ramesh, S. K. & Ideker, T. Integrative approaches for finding modular structure in biological networks. Nat. Rev. Genet. 14, 719\u2013732 (2013).","journal-title":"Nat. Rev. Genet."},{"issue":"Suppl 1","key":"85580_CR12","doi-asserted-by":"publisher","first-page":"S233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","volume":"18","author":"T Ideker","year":"2002","unstructured":"Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A. F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl 1), S233\u2013240 (2002).","journal-title":"Bioinformatics"},{"key":"85580_CR13","doi-asserted-by":"publisher","first-page":"e1009263","DOI":"10.1371\/journal.pcbi.1009263","volume":"17","author":"EM Novoa-Del-Toro","year":"2021","unstructured":"Novoa-Del-Toro, E. M. et al. A multi-objective genetic algorithm to find active modules in multiplex biological networks. PLoS Comput. Biol. 17, e1009263 (2021).","journal-title":"PLoS Comput. Biol."},{"key":"85580_CR14","doi-asserted-by":"publisher","first-page":"858","DOI":"10.3389\/fgene.2019.00858","volume":"10","author":"E Ulgen","year":"2019","unstructured":"Ulgen, E., Ozisik, O. & Sezerman, O. U. pathfindR: An R Package for Comprehensive Identification of Enriched pathways in Omics Data through active subnetworks. Front. Genet. 10, 858 (2019).","journal-title":"Front. Genet."},{"key":"85580_CR15","doi-asserted-by":"publisher","first-page":"e9593","DOI":"10.15252\/msb.20209593","volume":"17","author":"H Levi","year":"2021","unstructured":"Levi, H., Elkon, R. & Shamir, R. DOMINO: A network-based active module identification algorithm with reduced rate of false calls. Mol. Syst. Biol. 17, e9593 (2021).","journal-title":"Mol. Syst. Biol."},{"key":"85580_CR16","doi-asserted-by":"publisher","first-page":"Article17","DOI":"10.2202\/1544-6115.1128","volume":"4","author":"B Zhang","year":"2005","unstructured":"Zhang, B. & Horvath, S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4, Article17 (2005).","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"85580_CR17","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1186\/s12859-018-2351-7","volume":"19","author":"D Morselli Gysi","year":"2018","unstructured":"Morselli Gysi, D., Voigt, A., Fragoso, T. M., Almaas, E. & Nowick, K. wTO: An R package for computing weighted topological overlap and a consensus network with integrated visualization tool. BMC Bioinform. 19, 392 (2018).","journal-title":"BMC Bioinform."},{"key":"85580_CR18","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/msb.2011.99","volume":"8","author":"T Ideker","year":"2012","unstructured":"Ideker, T. & Krogan, N. J. Differential network biology. Mol. Syst. Biol. 8, 565 (2012).","journal-title":"Mol. Syst. Biol."},{"key":"85580_CR19","doi-asserted-by":"crossref","unstructured":"Li, J., Li, Y. X. & Li, Y. Y. Differential regulatory analysis based on coexpression network in cancer research. Biomed. Res. Int. 4241293 (2016). (2016).","DOI":"10.1155\/2016\/4241293"},{"key":"85580_CR20","doi-asserted-by":"publisher","first-page":"e0240523","DOI":"10.1371\/journal.pone.0240523","volume":"15","author":"D Morselli Gysi","year":"2020","unstructured":"Morselli Gysi, D. et al. Whole transcriptomic network analysis using co-expression Differential Network Analysis (CoDiNA). PLoS One. 15, e0240523 (2020).","journal-title":"PLoS One"},{"key":"85580_CR21","doi-asserted-by":"publisher","first-page":"3918","DOI":"10.1093\/bioinformatics\/btaa235","volume":"36","author":"HA de Weerd","year":"2020","unstructured":"de Weerd, H. A. et al. MODifieR: An Ensemble R Package for Inference of Disease modules from Transcriptomics Networks. Bioinformatics 36, 3918\u20133919 (2020).","journal-title":"Bioinformatics"},{"key":"85580_CR22","doi-asserted-by":"publisher","first-page":"e0143563","DOI":"10.1371\/journal.pone.0143563","volume":"10","author":"A Labadorf","year":"2015","unstructured":"Labadorf, A. et al. RNA sequence analysis of human Huntington Disease Brain reveals an extensive increase in inflammatory and developmental gene expression. PLoS One. 10, e0143563 (2015).","journal-title":"PLoS One"},{"key":"85580_CR23","doi-asserted-by":"publisher","first-page":"15005","DOI":"10.1038\/nrdp.2015.5","volume":"1","author":"GP Bates","year":"2015","unstructured":"Bates, G. P. et al. Huntington disease. Nat. Rev. Dis. Primers. 1, 15005 (2015).","journal-title":"Nat. Rev. Dis. Primers"},{"key":"85580_CR24","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1016\/0092-8674(93)90585-E","volume":"72","author":"ME MacDonald","year":"1993","unstructured":"MacDonald, M. E. et al. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington\u2019s disease chromosomes. The Huntington\u2019s Disease Collaborative Research Group. Cell 72, 971\u2013983 (1993).","journal-title":"Cell"},{"key":"85580_CR25","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1111\/ene.13413","volume":"25","author":"P McColgan","year":"2018","unstructured":"McColgan, P. & Tabrizi, S. J. Huntington\u2019s disease: A clinical review. Eur. J. Neurol. 25, 24\u201334 (2018).","journal-title":"Eur. J. Neurol."},{"key":"85580_CR26","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/1750-1172-5-40","volume":"5","author":"RAC Roos","year":"2010","unstructured":"Roos, R. A. C. Huntington\u2019s disease: A clinical review. Orphanet J. Rare Dis. 5, 40 (2010).","journal-title":"Orphanet J. Rare Dis."},{"key":"85580_CR27","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gkab1028","volume":"50","author":"M Gillespie","year":"2022","unstructured":"Gillespie, M. et al. The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50, D687\u2013D692 (2022).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR28","doi-asserted-by":"publisher","first-page":"W191","DOI":"10.1093\/nar\/gkz369","volume":"47","author":"U Raudvere","year":"2019","unstructured":"Raudvere, U. et al. g:Profiler: A web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 47, W191\u2013W198 (2019).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR29","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1186\/s12859-022-04828-2","volume":"23","author":"O Ozisik","year":"2022","unstructured":"Ozisik, O., T\u00e9r\u00e9zol, M. & Baudot, A. orsum: A Python package for filtering and comparing enrichment analyses using a simple principle. BMC Bioinform. 23, 293 (2022).","journal-title":"BMC Bioinform."},{"key":"85580_CR30","doi-asserted-by":"crossref","unstructured":"Ellrichmann, G., Reick, C., Saft, C. & Linker, R. A. The role of the immune system in Huntington\u2019s disease. Clin. Dev. Immunol. 541259 (2013). (2013).","DOI":"10.1155\/2013\/541259"},{"key":"85580_CR31","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1021\/acschemneuro.6b00042","volume":"7","author":"LF Clark","year":"2016","unstructured":"Clark, L. F. & Kodadek, T. The Immune System and Neuroinflammation as potential sources of blood-based biomarkers for Alzheimer\u2019s Disease, Parkinson\u2019s Disease, and Huntington\u2019s Disease. ACS Chem. Neurosci. 7, 520\u2013527 (2016).","journal-title":"ACS Chem. Neurosci."},{"key":"85580_CR32","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","volume":"33","author":"JR Conway","year":"2017","unstructured":"Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: An R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938\u20132940 (2017).","journal-title":"Bioinformatics"},{"key":"85580_CR33","doi-asserted-by":"crossref","unstructured":"Kandasamy, M., Reilmann, R., Winkler, J., Bogdahn, U. & Aigner, L. Transforming Growth Factor-Beta Signaling in the Neural Stem Cell Niche: A Therapeutic Target for Huntington\u2019s Disease. Neurol. Res. Int. 124256 (2011). (2011).","DOI":"10.1155\/2011\/124256"},{"key":"85580_CR34","doi-asserted-by":"publisher","first-page":"6703","DOI":"10.1074\/jbc.M110338200","volume":"277","author":"C Song","year":"2002","unstructured":"Song, C., Perides, G. & Liu, Y. F. Expression of full-length polyglutamine-expanded huntingtin disrupts growth factor receptor signaling in rat pheochromocytoma (PC12) cells. J. Biol. Chem. 277, 6703\u20136707 (2002).","journal-title":"J. Biol. Chem."},{"key":"85580_CR35","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1093\/hmg\/ddi443","volume":"15","author":"BL Apostol","year":"2006","unstructured":"Apostol, B. L. et al. Mutant huntingtin alters MAPK signaling pathways in PC12 and striatal cells: ERK1\/2 protects against mutant huntingtin-associated toxicity. Hum. Mol. Genet. 15, 273\u2013285 (2006).","journal-title":"Hum. Mol. Genet."},{"key":"85580_CR36","doi-asserted-by":"publisher","first-page":"4016","DOI":"10.1111\/ejn.15316","volume":"53","author":"A Freitas","year":"2021","unstructured":"Freitas, A. et al. Bioinformatic analysis of the human brain extracellular matrix proteome in neurodegenerative disorders. Eur. J. Neurosci. 53, 4016\u20134033 (2021).","journal-title":"Eur. J. Neurosci."},{"key":"85580_CR37","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1093\/brain\/awz363","volume":"143","author":"JD Crapser","year":"2020","unstructured":"Crapser, J. D. et al. Microglial depletion prevents extracellular matrix changes and striatal volume reduction in a model of Huntington\u2019s disease. Brain 143, 266\u2013288 (2020).","journal-title":"Brain"},{"key":"85580_CR38","doi-asserted-by":"publisher","first-page":"174","DOI":"10.9758\/cpn.2020.18.2.174","volume":"18","author":"A Ayka\u00e7","year":"2020","unstructured":"Ayka\u00e7, A. & \u015eehirli, A. \u00d6. The role of the SLC Transporters Protein in the neurodegenerative disorders. Clin. Psychopharmacol. Neurosci. 18, 174\u2013187 (2020).","journal-title":"Clin. Psychopharmacol. Neurosci."},{"key":"85580_CR39","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1093\/hmg\/ddl013","volume":"15","author":"A Hodges","year":"2006","unstructured":"Hodges, A. et al. Regional and cellular gene expression changes in human Huntington\u2019s disease brain. Hum. Mol. Genet. 15, 965\u2013977 (2006).","journal-title":"Hum. Mol. Genet."},{"key":"85580_CR40","doi-asserted-by":"publisher","first-page":"4552","DOI":"10.1523\/JNEUROSCI.5865-09.2010","volume":"30","author":"X Li","year":"2010","unstructured":"Li, X. et al. Aberrant Rab11-dependent trafficking of the neuronal glutamate transporter EAAC1 causes oxidative stress and cell death in Huntington\u2019s disease. J. Neurosci. 30, 4552\u20134561 (2010).","journal-title":"J. Neurosci."},{"key":"85580_CR41","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1002\/syn.1089","volume":"41","author":"M Suzuki","year":"2001","unstructured":"Suzuki, M., Desmond, T. J., Albin, R. L. & Frey, K. A. Vesicular neurotransmitter transporters in Huntington\u2019s disease: initial observations and comparison with traditional synaptic markers. Synapse 41, 329\u2013336 (2001).","journal-title":"Synapse"},{"key":"85580_CR42","doi-asserted-by":"publisher","first-page":"14763","DOI":"10.3390\/ijms232314763","volume":"23","author":"J Wu","year":"2022","unstructured":"Wu, J. et al. A Novel Huntington\u2019s Disease Assessment platform to support Future Drug Discovery and Development. Int. J. Mol. Sci. 23, 14763 (2022).","journal-title":"Int. J. Mol. Sci."},{"key":"85580_CR43","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1586\/ern.11.149","volume":"11","author":"J Jankovic","year":"2011","unstructured":"Jankovic, J. & Clarence-Smith, K. Tetrabenazine for the treatment of chorea and other hyperkinetic movement disorders. Expert Rev. Neurother. 11, 1509\u20131523 (2011).","journal-title":"Expert Rev. Neurother."},{"key":"85580_CR44","first-page":"319","volume":"11","author":"MH Periayah","year":"2017","unstructured":"Periayah, M. H., Halim, A. S. & Mat Saad, A. Z. Mechanism action of platelets and crucial blood coagulation pathways in Hemostasis. Int. J. Hematol. Oncol. Stem Cell. Res. 11, 319\u2013327 (2017).","journal-title":"Int. J. Hematol. Oncol. Stem Cell. Res."},{"key":"85580_CR45","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1136\/jnnp-2018-318854","volume":"90","author":"HL Denis","year":"2019","unstructured":"Denis, H. L. et al. Platelet abnormalities in Huntington\u2019s disease. J. Neurol. Neurosurg. Psychiatry. 90, 272\u2013283 (2019).","journal-title":"J. Neurol. Neurosurg. Psychiatry"},{"key":"85580_CR46","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1042\/BST0380552","volume":"38","author":"SL Hands","year":"2010","unstructured":"Hands, S. L., Mason, R., Sajjad, M. U., Giorgini, F. & Wyttenbach, A. Metallothioneins and copper metabolism are candidate therapeutic targets in Huntington\u2019s disease. Biochem. Soc. Trans. 38, 552\u2013558 (2010).","journal-title":"Biochem. Soc. Trans."},{"key":"85580_CR47","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/ng1503","volume":"37","author":"J Cornett","year":"2005","unstructured":"Cornett, J. et al. Polyglutamine expansion of huntingtin impairs its nuclear export. Nat. Genet. 37, 198\u2013204 (2005).","journal-title":"Nat. Genet."},{"key":"85580_CR48","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.neuron.2017.03.023","volume":"94","author":"JC Grima","year":"2017","unstructured":"Grima, J. C. et al. Mutant huntingtin disrupts the Nuclear Pore Complex. Neuron 94, 93\u2013107e6 (2017).","journal-title":"Neuron"},{"key":"85580_CR49","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1038\/s41582-022-00653-6","volume":"18","author":"AN Coyne","year":"2022","unstructured":"Coyne, A. N. & Rothstein, J. D. Nuclear pore complexes - a doorway to neural injury in neurodegeneration. Nat. Rev. Neurol. 18, 348\u2013362 (2022).","journal-title":"Nat. Rev. Neurol."},{"key":"85580_CR50","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1007\/s13311-022-01293-w","volume":"19","author":"O Spead","year":"2022","unstructured":"Spead, O., Zaepfel, B. L. & Rothstein, J. D. Nuclear Pore Dysfunction in Neurodegeneration. Neurotherapeutics 19, 1050\u20131060 (2022).","journal-title":"Neurotherapeutics"},{"key":"85580_CR51","doi-asserted-by":"publisher","first-page":"742763","DOI":"10.3389\/fncel.2021.742763","volume":"15","author":"J Lange","year":"2021","unstructured":"Lange, J. et al. Mislocalization of Nucleocytoplasmic Transport Proteins in Human Huntington\u2019s Disease PSC-Derived Striatal neurons. Front. Cell. Neurosci. 15, 742763 (2021).","journal-title":"Front. Cell. Neurosci."},{"key":"85580_CR52","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s40035-021-00240-7","volume":"10","author":"D Li","year":"2021","unstructured":"Li, D., McIntosh, C. S., Mastaglia, F. L., Wilton, S. D. & Aung-Htut, M. T. Neurodegenerative diseases: A hotbed for splicing defects and the potential therapies. Transl Neurodegener. 10, 16 (2021).","journal-title":"Transl Neurodegener"},{"key":"85580_CR53","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/s41583-023-00717-6","volume":"24","author":"D Nikom","year":"2023","unstructured":"Nikom, D. & Zheng, S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat. Rev. Neurosci. 24, 457\u2013473 (2023).","journal-title":"Nat. Rev. Neurosci."},{"key":"85580_CR54","doi-asserted-by":"publisher","first-page":"104720","DOI":"10.1016\/j.ebiom.2023.104720","volume":"94","author":"V Tano","year":"2023","unstructured":"Tano, V. et al. Widespread dysregulation of mRNA splicing implicates RNA processing in the development and progression of Huntington\u2019s disease. EBioMedicine 94, 104720 (2023).","journal-title":"EBioMedicine"},{"key":"85580_CR55","doi-asserted-by":"publisher","first-page":"487","DOI":"10.3390\/toxins13070487","volume":"13","author":"A Heinz","year":"2021","unstructured":"Heinz, A., Nabariya, D. K. & Krauss, S. Huntingtin and its role in mechanisms of RNA-Mediated toxicity. Toxins (Basel). 13, 487 (2021).","journal-title":"Toxins (Basel)"},{"key":"85580_CR56","doi-asserted-by":"publisher","first-page":"1869","DOI":"10.1016\/j.jmb.2019.01.034","volume":"431","author":"J Schilling","year":"2019","unstructured":"Schilling, J. et al. Deregulated splicing is a major mechanism of RNA-Induced toxicity in Huntington\u2019s Disease. J. Mol. Biol. 431, 1869\u20131877 (2019).","journal-title":"J. Mol. Biol."},{"key":"85580_CR57","doi-asserted-by":"publisher","first-page":"2366","DOI":"10.1073\/pnas.1221891110","volume":"110","author":"K Sathasivam","year":"2013","unstructured":"Sathasivam, K. et al. Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease. Proc. Natl. Acad. Sci. U S A. 110, 2366\u20132370 (2013).","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"85580_CR58","doi-asserted-by":"publisher","first-page":"14057","DOI":"10.1038\/s41598-020-71111-w","volume":"10","author":"MA Mason","year":"2020","unstructured":"Mason, M. A. et al. Silencing Srsf6 does not modulate incomplete splicing of the huntingtin gene in Huntington\u2019s disease models. Sci. Rep. 10, 14057 (2020).","journal-title":"Sci. Rep."},{"key":"85580_CR59","doi-asserted-by":"publisher","first-page":"RRN1255","DOI":"10.1371\/currents.RRN1255","volume":"3","author":"E Teuling","year":"2011","unstructured":"Teuling, E. et al. Modifiers of mutant huntingtin aggregation: functional conservation of C. Elegans-modifiers of polyglutamine aggregation. PLoS Curr. 3, RRN1255 (2011).","journal-title":"PLoS Curr."},{"key":"85580_CR60","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","volume":"51","author":"D Szklarczyk","year":"2023","unstructured":"Szklarczyk, D. et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638\u2013D646 (2023).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR61","doi-asserted-by":"publisher","first-page":"10373","DOI":"10.1038\/s41598-022-14169-y","volume":"12","author":"AC Pfalzer","year":"2022","unstructured":"Pfalzer, A. C. et al. Alterations in metal homeostasis occur prior to canonical markers in Huntington disease. Sci. Rep. 12, 10373 (2022).","journal-title":"Sci. Rep."},{"key":"85580_CR62","doi-asserted-by":"publisher","first-page":"101152","DOI":"10.1016\/j.arr.2020.101152","volume":"63","author":"M Scholefield","year":"2020","unstructured":"Scholefield, M., Unwin, R. D. & Cooper, G. J. S. Shared perturbations in the metallome and metabolome of Alzheimer\u2019s, Parkinson\u2019s, Huntington\u2019s, and dementia with Lewy bodies: A systematic review. Ageing Res. Rev. 63, 101152 (2020).","journal-title":"Ageing Res. Rev."},{"key":"85580_CR63","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1039\/d0mt00081g","volume":"12","author":"AC Pfalzer","year":"2020","unstructured":"Pfalzer, A. C. et al. Huntington\u2019s disease genotype suppresses global manganese-responsive processes in pre-manifest and manifest YAC128 mice. Metallomics 12, 1118\u20131130 (2020).","journal-title":"Metallomics"},{"key":"85580_CR64","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.semcdb.2017.05.006","volume":"68","author":"S Sakuma","year":"2017","unstructured":"Sakuma, S. & D\u2019Angelo, M. A. The roles of the nuclear pore complex in cellular dysfunction, aging and disease. Semin Cell. Dev. Biol. 68, 72\u201384 (2017).","journal-title":"Semin Cell. Dev. Biol."},{"key":"85580_CR65","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of Fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"85580_CR66","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/1471-2105-9-559","volume":"9","author":"P Langfelder","year":"2008","unstructured":"Langfelder, P. & Horvath, S. WGCNA: An R package for weighted correlation network analysis. BMC Bioinform. 9, 559 (2008).","journal-title":"BMC Bioinform."},{"key":"85580_CR67","doi-asserted-by":"publisher","first-page":"3157","DOI":"10.1016\/j.ygeno.2020.05.026","volume":"112","author":"T Abbassi-Daloii","year":"2020","unstructured":"Abbassi-Daloii, T., Kan, H. E., Raz, V. & 't Hoen, P. A. C. Recommendations for the analysis of gene expression data to identify intrinsic differences between similar tissues. Genomics 112, 3157\u20133165 (2020).","journal-title":"Genomics"},{"key":"85580_CR68","doi-asserted-by":"crossref","unstructured":"Kutmon, M., Ehrhart, F., Willighagen, E. L., Evelo, C. T. & Coort, S. L. CyTargetLinker app update: A flexible solution for network extension in Cytoscape. F1000Res. 7, ELIXIR-743 (2018).","DOI":"10.12688\/f1000research.14613.1"},{"key":"85580_CR69","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/pro.3978","volume":"30","author":"R Oughtred","year":"2021","unstructured":"Oughtred, R. et al. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 30, 187\u2013200 (2021).","journal-title":"Protein Sci."},{"key":"85580_CR70","doi-asserted-by":"publisher","first-page":"8794","DOI":"10.1038\/s41598-021-87987-1","volume":"11","author":"L Pio-Lopez","year":"2021","unstructured":"Pio-Lopez, L., Valdeolivas, A., Tichit, L., Remy, \u00c9. & Baudot, A. MultiVERSE: A multiplex and multiplex-heterogeneous network embedding approach. Sci. Rep. 11, 8794 (2021).","journal-title":"Sci. Rep."},{"key":"85580_CR71","doi-asserted-by":"publisher","first-page":"W529","DOI":"10.1093\/nar\/gkw363","volume":"44","author":"D Alonso-L\u00f3pez","year":"2016","unstructured":"Alonso-L\u00f3pez, D. et al. APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res. 44, W529\u2013535 (2016).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR72","doi-asserted-by":"crossref","unstructured":"Alonso-L\u00f3pez, D. et al. APID database: Redefining protein-protein interaction experimental evidences and binary interactomes. Database (Oxford) baz005 (2019). (2019).","DOI":"10.1093\/database\/baz005"},{"key":"85580_CR73","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1038\/s41586-020-2188-x","volume":"580","author":"K Luck","year":"2020","unstructured":"Luck, K. et al. A reference map of the human binary protein interactome. Nature 580, 402\u2013408 (2020).","journal-title":"Nature"},{"key":"85580_CR74","doi-asserted-by":"publisher","first-page":"e58","DOI":"10.1158\/0008-5472.CAN-17-0606","volume":"77","author":"D Pratt","year":"2017","unstructured":"Pratt, D. et al. NDEx 2.0: A clearinghouse for Research on Cancer pathways. Cancer Res. 77, e58\u2013e61 (2017).","journal-title":"Cancer Res."},{"key":"85580_CR75","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1016\/j.cels.2018.03.001","volume":"6","author":"JK Huang","year":"2018","unstructured":"Huang, J. K. et al. Systematic evaluation of Molecular Networks for Discovery of Disease genes. Cell. Syst. 6, 484\u2013495e5 (2018).","journal-title":"Cell. Syst."},{"key":"85580_CR76","doi-asserted-by":"publisher","first-page":"932","DOI":"10.15252\/msb.20167490","volume":"13","author":"K Drew","year":"2017","unstructured":"Drew, K. et al. Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol. Syst. Biol. 13, 932 (2017).","journal-title":"Mol. Syst. Biol."},{"key":"85580_CR77","doi-asserted-by":"publisher","first-page":"D559","DOI":"10.1093\/nar\/gky973","volume":"47","author":"M Giurgiu","year":"2019","unstructured":"Giurgiu, M. et al. CORUM: The comprehensive resource of mammalian protein complexes-2019. Nucleic Acids Res. 47, D559\u2013D563 (2019).","journal-title":"Nucleic Acids Res."},{"key":"85580_CR78","doi-asserted-by":"publisher","first-page":"e9923","DOI":"10.15252\/msb.20209923","volume":"17","author":"D T\u00fcrei","year":"2021","unstructured":"T\u00fcrei, D. et al. Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol. Syst. Biol. 17, e9923 (2021).","journal-title":"Mol. Syst. Biol."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-85580-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-85580-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-85580-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T07:07:10Z","timestamp":1736406430000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-85580-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,9]]},"references-count":78,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["85580"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-85580-4","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,9]]},"assertion":[{"value":"26 June 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 January 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1412"}}