{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T06:16:17Z","timestamp":1771654577837,"version":"3.50.1"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T00:00:00Z","timestamp":1549411200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T00:00:00Z","timestamp":1549411200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100003710","name":"Korea Health Industry Development Institute","doi-asserted-by":"publisher","award":["HI15C0001"],"award-info":[{"award-number":["HI15C0001"]}],"id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003710","name":"Korea Health Industry Development Institute","doi-asserted-by":"publisher","award":["HC15C1129"],"award-info":[{"award-number":["HC15C1129"]}],"id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2014R1A5A2009242"],"award-info":[{"award-number":["2014R1A5A2009242"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2015R1C1A1A02037367"],"award-info":[{"award-number":["2015R1C1A1A02037367"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2016R1A2B4006575"],"award-info":[{"award-number":["2016R1A2B4006575"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Long-term peritoneal dialysis is associated with progressive fibrosis of the peritoneum. Epithelial-mesenchymal transition (EMT) of mesothelial cells is an important mechanism involved in peritoneal fibrosis, and TGF-\u03b21 is considered central in this process. However, targeting currently known TGF-\u03b21-associated pathways has not proven effective to date. Therefore, there are still gaps in understanding the mechanisms underlying TGF-\u03b21-associated EMT and peritoneal fibrosis. We conducted network-based integrated analysis of transcriptomic and proteomic data to systemically characterize the molecular signature of TGF-\u03b21-stimulated human peritoneal mesothelial cells (HPMCs). To increase the power of the data, multiple expression datasets of TGF-\u03b21-stimulated human cells were employed, and extended based on a human functional gene network. Dense network sub-modules enriched with differentially expressed genes by TGF-\u03b21 stimulation were prioritized and genes of interest were selected for functional analysis in HPMCs. Through integrated analysis, ECM constituents and oxidative stress-related genes were shown to be the top-ranked genes as expected. Among top-ranked sub-modules, <jats:italic>TNFAIP6<\/jats:italic>, <jats:italic>ZC3H12A<\/jats:italic>, and <jats:italic>NNT<\/jats:italic> were validated in HPMCs to be involved in regulation of E-cadherin, ZO-1, fibronectin, and \u03b1SMA expression. The present data shows the validity of network-based integrated analysis in discovery of novel players in TGF-\u03b21-induced EMT in peritoneal mesothelial cells, which may serve as new prognostic markers and therapeutic targets for peritoneal dialysis patients.<\/jats:p>","DOI":"10.1038\/s41598-018-37101-9","type":"journal-article","created":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T11:04:47Z","timestamp":1549451087000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Network-based integrated analysis of omics data reveal novel players of TGF-\u03b21-induced EMT in human peritoneal mesothelial cells"],"prefix":"10.1038","volume":"9","author":[{"given":"Soo Min","family":"Han","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hye-Myung","family":"Ryu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinjoo","family":"Suh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kong-Joo","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soon-Youn","family":"Choi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sangdun","family":"Choi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong-Lim","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joo Young","family":"Huh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hunjoo","family":"Ha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,2,6]]},"reference":[{"key":"37101_CR1","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1053\/j.ajkd.2005.08.011","volume":"46","author":"LS Aroeira","year":"2005","unstructured":"Aroeira, L. S. et al. Mesenchymal conversion of mesothelial cells as a mechanism responsible for high solute transport rate in peritoneal dialysis: role of vascular endothelial growth factor. American journal of kidney diseases: the official journal of the National Kidney Foundation 46, 938\u2013948, https:\/\/doi.org\/10.1053\/j.ajkd.2005.08.011 (2005).","journal-title":"American journal of kidney diseases: the official journal of the National Kidney Foundation"},{"issue":"Suppl 5","key":"37101_CR2","doi-asserted-by":"crossref","first-page":"S29","DOI":"10.1177\/089686080802805S06","volume":"28","author":"LS Aroeira","year":"2008","unstructured":"Aroeira, L. S. et al. Characterization of epithelial-to-mesenchymal transition of mesothelial cells in a mouse model of chronic peritoneal exposure to high glucose dialysate. Peritoneal dialysis international: journal of the International Society for Peritoneal Dialysis 28(Suppl 5), S29\u201333 (2008).","journal-title":"Peritoneal dialysis international: journal of the International Society for Peritoneal Dialysis"},{"key":"37101_CR3","doi-asserted-by":"publisher","first-page":"2004","DOI":"10.1681\/ASN.2006111292","volume":"18","author":"LS Aroeira","year":"2007","unstructured":"Aroeira, L. S. et al. Epithelial to mesenchymal transition and peritoneal membrane failure in peritoneal dialysis patients: pathologic significance and potential therapeutic interventions. Journal of the American Society of Nephrology: JASN 18, 2004\u20132013, https:\/\/doi.org\/10.1681\/ASN.2006111292 (2007).","journal-title":"Journal of the American Society of Nephrology: JASN"},{"issue":"Suppl 2","key":"37101_CR4","doi-asserted-by":"crossref","first-page":"S123","DOI":"10.1177\/089686080902902S24","volume":"29","author":"YL Kim","year":"2009","unstructured":"Kim, Y. L. Update on mechanisms of ultrafiltration failure. Peritoneal dialysis international: journal of the International Society for Peritoneal Dialysis 29(Suppl 2), S123\u2013127 (2009).","journal-title":"Peritoneal dialysis international: journal of the International Society for Peritoneal Dialysis"},{"key":"37101_CR5","doi-asserted-by":"publisher","unstructured":"Del Peso, G. et al. Epithelial-to-mesenchymal transition of mesothelial cells is an early event during peritoneal dialysis and is associated with high peritoneal transport. Kidney international. Supplement, S26\u201333, https:\/\/doi.org\/10.1038\/sj.ki.5002598 (2008).","DOI":"10.1038\/sj.ki.5002598"},{"key":"37101_CR6","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1056\/NEJMoa020809","volume":"348","author":"M Yanez-Mo","year":"2003","unstructured":"Yanez-Mo, M. et al. Peritoneal dialysis and epithelial-to-mesenchymal transition of mesothelial cells. The New England journal of medicine 348, 403\u2013413, https:\/\/doi.org\/10.1056\/NEJMoa020809 (2003).","journal-title":"The New England journal of medicine"},{"key":"37101_CR7","doi-asserted-by":"publisher","first-page":"e61165","DOI":"10.1371\/journal.pone.0061165","volume":"8","author":"J Loureiro","year":"2013","unstructured":"Loureiro, J. et al. Tamoxifen ameliorates peritoneal membrane damage by blocking mesothelial to mesenchymal transition in peritoneal dialysis. PloS one 8, e61165, https:\/\/doi.org\/10.1371\/journal.pone.0061165 (2013).","journal-title":"PloS one"},{"key":"37101_CR8","first-page":"347","volume":"12","author":"N Di Paolo","year":"1999","unstructured":"Di Paolo, N. & Garosi, G. Peritoneal sclerosis. Journal of nephrology 12, 347\u2013361 (1999).","journal-title":"Journal of nephrology"},{"key":"37101_CR9","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1016\/S0272-6386(00)70011-4","volume":"35","author":"KN Lai","year":"2000","unstructured":"Lai, K. N. et al. Changes of cytokine profiles during peritonitis in patients on continuous ambulatory peritoneal dialysis. American journal of kidney diseases: the official journal of the National Kidney Foundation 35, 644\u2013652 (2000).","journal-title":"American journal of kidney diseases: the official journal of the National Kidney Foundation"},{"key":"37101_CR10","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1159\/000232937","volume":"28","author":"AS Gangji","year":"2009","unstructured":"Gangji, A. S., Brimble, K. S. & Margetts, P. J. Association between markers of inflammation, fibrosis and hypervolemia in peritoneal dialysis patients. Blood purification 28, 354\u2013358, https:\/\/doi.org\/10.1159\/000232937 (2009).","journal-title":"Blood purification"},{"key":"37101_CR11","doi-asserted-by":"publisher","first-page":"e71","DOI":"10.1159\/000142529","volume":"109","author":"Q Yao","year":"2008","unstructured":"Yao, Q. et al. The role of the TGF\/Smad signaling pathway in peritoneal fibrosis induced by peritoneal dialysis solutions. Nephron. Experimental nephrology 109, e71\u201378, https:\/\/doi.org\/10.1159\/000142529 (2008).","journal-title":"Nephron. Experimental nephrology"},{"key":"37101_CR12","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1681\/ASN.2010111197","volume":"22","author":"J Loureiro","year":"2011","unstructured":"Loureiro, J. et al. Blocking TGF-beta1 protects the peritoneal membrane from dialysate-induced damage. Journal of the American Society of Nephrology: JASN 22, 1682\u20131695, https:\/\/doi.org\/10.1681\/ASN.2010111197 (2011).","journal-title":"Journal of the American Society of Nephrology: JASN"},{"key":"37101_CR13","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1038\/nrm3758","volume":"15","author":"S Lamouille","year":"2014","unstructured":"Lamouille, S., Xu, J. & Derynck, R. Molecular mechanisms of epithelial-mesenchymal transition. Nature reviews. Molecular cell biology 15, 178\u2013196, https:\/\/doi.org\/10.1038\/nrm3758 (2014).","journal-title":"Nature reviews. Molecular cell biology"},{"key":"37101_CR14","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1159\/000203362","volume":"30","author":"Y Sun","year":"2009","unstructured":"Sun, Y. et al. Treatment of established peritoneal fibrosis by gene transfer of Smad7 in a rat model of peritoneal dialysis. American journal of nephrology 30, 84\u201394, https:\/\/doi.org\/10.1159\/000203362 (2009).","journal-title":"American journal of nephrology"},{"key":"37101_CR15","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1681\/ASN.2008040424","volume":"20","author":"MA Yu","year":"2009","unstructured":"Yu, M. A. et al. HGF and BMP-7 ameliorate high glucose-induced epithelial-to-mesenchymal transition of peritoneal mesothelium. Journal of the American Society of Nephrology: JASN 20, 567\u2013581, https:\/\/doi.org\/10.1681\/ASN.2008040424 (2009).","journal-title":"Journal of the American Society of Nephrology: JASN"},{"key":"37101_CR16","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1093\/ndt\/gfp618","volume":"25","author":"J Loureiro","year":"2010","unstructured":"Loureiro, J. et al. BMP-7 blocks mesenchymal conversion of mesothelial cells and prevents peritoneal damage induced by dialysis fluid exposure. Nephrology, dialysis, transplantation: official publication of the European Dialysis and Transplant Association - European Renal Association 25, 1098\u20131108, https:\/\/doi.org\/10.1093\/ndt\/gfp618 (2010).","journal-title":"Nephrology, dialysis, transplantation: official publication of the European Dialysis and Transplant Association - European Renal Association"},{"key":"37101_CR17","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/ncponc0176","volume":"2","author":"R Simon","year":"2005","unstructured":"Simon, R. Bioinformatics in cancer therapeutics\u2013hype or hope? Nature clinical practice. Oncology 2, 223, https:\/\/doi.org\/10.1038\/ncponc0176 (2005).","journal-title":"Nature clinical practice. Oncology"},{"key":"37101_CR18","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1158\/1078-0432.CCR-12-1139","volume":"19","author":"J Botling","year":"2013","unstructured":"Botling, J. et al. Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. Clinical cancer research: an official journal of the American Association for Cancer Research 19, 194\u2013204, https:\/\/doi.org\/10.1158\/1078-0432.CCR-12-1139 (2013).","journal-title":"Clinical cancer research: an official journal of the American Association for Cancer Research"},{"key":"37101_CR19","doi-asserted-by":"publisher","first-page":"2793","DOI":"10.1200\/JCO.2008.19.7053","volume":"27","author":"S Tomida","year":"2009","unstructured":"Tomida, S. et al. Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis. Journal of clinical oncology: official journal of the American Society of Clinical Oncology 27, 2793\u20132799, https:\/\/doi.org\/10.1200\/JCO.2008.19.7053 (2009).","journal-title":"Journal of clinical oncology: official journal of the American Society of Clinical Oncology"},{"key":"37101_CR20","doi-asserted-by":"publisher","first-page":"pe13","DOI":"10.1126\/scisignal.2003684","volume":"6","author":"MB Yaffe","year":"2013","unstructured":"Yaffe, M. B. The scientific drunk and the lamppost: massive sequencing efforts in cancer discovery and treatment. Science signaling 6, pe13, https:\/\/doi.org\/10.1126\/scisignal.2003684 (2013).","journal-title":"Science signaling"},{"key":"37101_CR21","doi-asserted-by":"publisher","first-page":"1234850","DOI":"10.1126\/science.1234850","volume":"342","author":"MA Nieto","year":"2013","unstructured":"Nieto, M. A. Epithelial plasticity: a common theme in embryonic and cancer cells. Science 342, 1234850, https:\/\/doi.org\/10.1126\/science.1234850 (2013).","journal-title":"Science"},{"key":"37101_CR22","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1101\/gr.118992.110","volume":"21","author":"I Lee","year":"2011","unstructured":"Lee, I., Blom, U. M., Wang, P. I., Shim, J. E. & Marcotte, E. M. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome research 21, 1109\u20131121, https:\/\/doi.org\/10.1101\/gr.118992.110 (2011).","journal-title":"Genome research"},{"key":"37101_CR23","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-015-0207-5","volume":"16","author":"Y Itoigawa","year":"2015","unstructured":"Itoigawa, Y. et al. TWEAK enhances TGF-beta-induced epithelial-mesenchymal transition in human bronchial epithelial cells. Respiratory research 16, 48, https:\/\/doi.org\/10.1186\/s12931-015-0207-5 (2015).","journal-title":"Respiratory research"},{"key":"37101_CR24","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.1002\/jcp.24905","volume":"230","author":"S Berzal","year":"2015","unstructured":"Berzal, S. et al. TNF-related weak inducer of apoptosis (TWEAK) regulates junctional proteins in tubular epithelial cells via canonical NF-kappaB pathway and ERK activation. Journal of cellular physiology 230, 1580\u20131593, https:\/\/doi.org\/10.1002\/jcp.24905 (2015).","journal-title":"Journal of cellular physiology"},{"key":"37101_CR25","doi-asserted-by":"publisher","first-page":"1344","DOI":"10.1093\/carcin\/bgq108","volume":"31","author":"M Natsuizaka","year":"2010","unstructured":"Natsuizaka, M. et al. Insulin-like growth factor-binding protein-3 promotes transforming growth factor-{beta}1-mediated epithelial-to-mesenchymal transition and motility in transformed human esophageal cells. Carcinogenesis 31, 1344\u20131353, https:\/\/doi.org\/10.1093\/carcin\/bgq108 (2010).","journal-title":"Carcinogenesis"},{"key":"37101_CR26","doi-asserted-by":"publisher","first-page":"3112","DOI":"10.1080\/15384101.2015.1078034","volume":"14","author":"J Zhao","year":"2015","unstructured":"Zhao, J. et al. Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer. Cell cycle 14, 3112\u20133123, https:\/\/doi.org\/10.1080\/15384101.2015.1078034 (2015).","journal-title":"Cell cycle"},{"key":"37101_CR27","doi-asserted-by":"publisher","unstructured":"Cai, Q. et al. Long non-coding RNA LINC00152 promotes gallbladder cancer metastasis and epithelial-mesenchymal transition by regulating HIF-1alpha via miR-138. Open biology 7, https:\/\/doi.org\/10.1098\/rsob.160247 (2017).","DOI":"10.1098\/rsob.160247"},{"key":"37101_CR28","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1038\/ng.2299","volume":"44","author":"E Meimaridou","year":"2012","unstructured":"Meimaridou, E. et al. Mutations in NNT encoding nicotinamide nucleotide transhydrogenase cause familial glucocorticoid deficiency. Nature genetics 44, 740\u2013742, https:\/\/doi.org\/10.1038\/ng.2299 (2012).","journal-title":"Nature genetics"},{"key":"37101_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-05836-6","volume":"7","author":"HS Shin","year":"2017","unstructured":"Shin, H. S. et al. Metformin ameliorates the Phenotype Transition of Peritoneal Mesothelial Cells and Peritoneal Fibrosis via a modulation of Oxidative Stress. Scientific reports 7, 5690, https:\/\/doi.org\/10.1038\/s41598-017-05836-6 (2017).","journal-title":"Scientific reports"},{"key":"37101_CR30","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1172\/JCI44595","volume":"121","author":"W Kriz","year":"2011","unstructured":"Kriz, W., Kaissling, B. & Le Hir, M. Epithelial-mesenchymal transition (EMT) in kidney fibrosis: fact or fantasy? The Journal of clinical investigation 121, 468\u2013474 (2011).","journal-title":"The Journal of clinical investigation"},{"key":"37101_CR31","doi-asserted-by":"publisher","unstructured":"Taura, K., Iwaisako, K., Hatano, E. & Uemoto, S. Controversies over the Epithelial-to-Mesenchymal Transition in Liver Fibrosis. Journal of clinical medicine 5, https:\/\/doi.org\/10.3390\/jcm5010009 (2016).","DOI":"10.3390\/jcm5010009"},{"issue":"Suppl 2","key":"37101_CR32","doi-asserted-by":"publisher","first-page":"ii2","DOI":"10.1093\/ndt\/gfl183","volume":"21","author":"R Selgas","year":"2006","unstructured":"Selgas, R. et al. Epithelial-to-mesenchymal transition of the mesothelial cell\u2013its role in the response of the peritoneum to dialysis. Nephrology, dialysis, transplantation: official publication of the European Dialysis and Transplant Association - European Renal Association 21(Suppl 2), ii2\u20137, https:\/\/doi.org\/10.1093\/ndt\/gfl183 (2006).","journal-title":"Nephrology, dialysis, transplantation: official publication of the European Dialysis and Transplant Association - European Renal Association"},{"key":"37101_CR33","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1111\/j.1523-1755.2004.00491.x","volume":"65","author":"HB Lee","year":"2004","unstructured":"Lee, H. B., Yu, M. R., Song, J. S. & Ha, H. Reactive oxygen species amplify protein kinase C signaling in high glucose-induced fibronectin expression by human peritoneal mesothelial cells. Kidney international 65, 1170\u20131179, https:\/\/doi.org\/10.1111\/j.1523-1755.2004.00491.x (2004).","journal-title":"Kidney international"},{"key":"37101_CR34","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.krcp.2015.03.005","volume":"34","author":"M Yu","year":"2015","unstructured":"Yu, M. et al. Effect of aldosterone on epithelial-to-mesenchymal transition of human peritoneal mesothelial cells. Kidney research and clinical practice 34, 83\u201392, https:\/\/doi.org\/10.1016\/j.krcp.2015.03.005 (2015).","journal-title":"Kidney research and clinical practice"},{"key":"37101_CR35","doi-asserted-by":"publisher","first-page":"e35510","DOI":"10.1371\/journal.pone.0035510","volume":"7","author":"I Drozdov","year":"2012","unstructured":"Drozdov, I. et al. Functional and topological properties in hepatocellular carcinoma transcriptome. PloS one 7, e35510, https:\/\/doi.org\/10.1371\/journal.pone.0035510 (2012).","journal-title":"PloS one"},{"key":"37101_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-5-r52","volume":"14","author":"M D\u2019Antonio","year":"2013","unstructured":"D\u2019Antonio, M. & Ciccarelli, F. D. Integrated analysis of recurrent properties of cancer genes to identify novel drivers. Genome biology 14, R52, https:\/\/doi.org\/10.1186\/gb-2013-14-5-r52 (2013).","journal-title":"Genome biology"},{"key":"37101_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms6893","volume":"5","author":"SM Dhanasekaran","year":"2014","unstructured":"Dhanasekaran, S. M. et al. Transcriptome meta-analysis of lung cancer reveals recurrent aberrations in NRG1 and Hippo pathway genes. Nature communications 5, 5893, https:\/\/doi.org\/10.1038\/ncomms6893 (2014).","journal-title":"Nature communications"},{"key":"37101_CR38","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-460","volume":"11","author":"D Nitsch","year":"2010","unstructured":"Nitsch, D., Goncalves, J. P., Ojeda, F., de Moor, B. & Moreau, Y. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC bioinformatics 11, 460, https:\/\/doi.org\/10.1186\/1471-2105-11-460 (2010).","journal-title":"BMC bioinformatics"},{"issue":"Suppl 9","key":"37101_CR39","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-16-S9-S2","volume":"16","author":"F Browne","year":"2015","unstructured":"Browne, F., Wang, H. & Zheng, H. A computational framework for the prioritization of disease-gene candidates. BMC genomics 16(Suppl 9), S2, https:\/\/doi.org\/10.1186\/1471-2164-16-S9-S2 (2015).","journal-title":"BMC genomics"},{"key":"37101_CR40","doi-asserted-by":"publisher","first-page":"1172","DOI":"10.3892\/mmr.2017.6154","volume":"15","author":"T Wang","year":"2017","unstructured":"Wang, T. et al. Knockdown of the differentially expressed gene TNFRSF12A inhibits hepatocellular carcinoma cell proliferation and migration in vitro. Molecular medicine reports 15, 1172\u20131178, https:\/\/doi.org\/10.3892\/mmr.2017.6154 (2017).","journal-title":"Molecular medicine reports"},{"key":"37101_CR41","doi-asserted-by":"publisher","first-page":"78507","DOI":"10.18632\/oncotarget.19659","volume":"8","author":"Z Cao","year":"2017","unstructured":"Cao, Z., Koochekpour, S., Strup, S. E. & Kyprianou, N. Reversion of epithelial-mesenchymal transition by a novel agent DZ-50 via IGF binding protein-3 in prostate cancer cells. Oncotarget 8, 78507\u201378519, https:\/\/doi.org\/10.18632\/oncotarget.19659 (2017).","journal-title":"Oncotarget"},{"key":"37101_CR42","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1016\/j.celrep.2013.09.015","volume":"5","author":"JA Wawrzyniak","year":"2013","unstructured":"Wawrzyniak, J. A. et al. A purine nucleotide biosynthesis enzyme guanosine monophosphate reductase is a suppressor of melanoma invasion. Cell reports 5, 493\u2013507, https:\/\/doi.org\/10.1016\/j.celrep.2013.09.015 (2013).","journal-title":"Cell reports"},{"key":"37101_CR43","doi-asserted-by":"publisher","first-page":"e0126285","DOI":"10.1371\/journal.pone.0126285","volume":"10","author":"Q Ying","year":"2015","unstructured":"Ying, Q. et al. Quantitative proteomic analysis reveals that anti-cancer effects of selenium-binding protein 1 in vivo are associated with metabolic pathways. PloS one 10, e0126285, https:\/\/doi.org\/10.1371\/journal.pone.0126285 (2015).","journal-title":"PloS one"},{"key":"37101_CR44","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1007\/s12011-014-0091-8","volume":"161","author":"J Liu","year":"2014","unstructured":"Liu, J. et al. Selenium suppresses lipopolysaccharide-induced fibrosis in peritoneal mesothelial cells through inhibition of epithelial-to-mesenchymal transition. Biological trace element research 161, 202\u2013209, https:\/\/doi.org\/10.1007\/s12011-014-0091-8 (2014).","journal-title":"Biological trace element research"},{"key":"37101_CR45","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1016\/j.biocel.2011.08.009","volume":"43","author":"G Bommaya","year":"2011","unstructured":"Bommaya, G., Meran, S., Krupa, A., Phillips, A. O. & Steadman, R. Tumour necrosis factor-stimulated gene (TSG)\u22126 controls epithelial-mesenchymal transition of proximal tubular epithelial cells. The international journal of biochemistry & cell biology 43, 1739\u20131746, https:\/\/doi.org\/10.1016\/j.biocel.2011.08.009 (2011).","journal-title":"The international journal of biochemistry & cell biology"},{"key":"37101_CR46","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.mehy.2013.03.036","volume":"81","author":"F Zhang","year":"2013","unstructured":"Zhang, F. et al. New insights into the pathogenesis and treatment of peritoneal fibrosis: a potential role of Wnt\/beta-catenin induced epithelial to mesenchymal transition and stem cells for therapy. Medical hypotheses 81, 97\u2013100, https:\/\/doi.org\/10.1016\/j.mehy.2013.03.036 (2013).","journal-title":"Medical hypotheses"},{"key":"37101_CR47","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1038\/nature07924","volume":"458","author":"K Matsushita","year":"2009","unstructured":"Matsushita, K. et al. Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458, 1185\u20131190, https:\/\/doi.org\/10.1038\/nature07924 (2009).","journal-title":"Nature"},{"key":"37101_CR48","doi-asserted-by":"publisher","first-page":"4905","DOI":"10.1158\/0008-5472.CAN-16-3190","volume":"77","author":"P Marona","year":"2017","unstructured":"Marona, P. et al. MCPIP1 Downregulation in Clear Cell Renal Cell Carcinoma Promotes Vascularization and Metastatic Progression. Cancer research 77, 4905\u20134920, https:\/\/doi.org\/10.1158\/0008-5472.CAN-16-3190 (2017).","journal-title":"Cancer research"},{"key":"37101_CR49","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1007\/s10456-017-9540-2","volume":"20","author":"J Ligeza","year":"2017","unstructured":"Ligeza, J. et al. MCPIP1 contributes to clear cell renal cell carcinomas development. Angiogenesis 20, 325\u2013340, https:\/\/doi.org\/10.1007\/s10456-017-9540-2 (2017).","journal-title":"Angiogenesis"},{"key":"37101_CR50","doi-asserted-by":"publisher","first-page":"6268","DOI":"10.1158\/0008-5472.CAN-12-2270","volume":"72","author":"M Romagnoli","year":"2012","unstructured":"Romagnoli, M. et al. Epithelial-to-mesenchymal transition induced by TGF-beta1 is mediated by Blimp-1-dependent repression of BMP-5. Cancer research 72, 6268\u20136278, https:\/\/doi.org\/10.1158\/0008-5472.CAN-12-2270 (2012).","journal-title":"Cancer research"},{"key":"37101_CR51","doi-asserted-by":"publisher","first-page":"R187","DOI":"10.1186\/bcr640","volume":"5","author":"L Xie","year":"2003","unstructured":"Xie, L. et al. Transforming growth factor beta-regulated gene expression in a mouse mammary gland epithelial cell line. Breast cancer research: BCR 5, R187\u2013198, https:\/\/doi.org\/10.1186\/bcr640 (2003).","journal-title":"Breast cancer research: BCR"},{"key":"37101_CR52","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1158\/1541-7786.MCR-16-0313","volume":"15","author":"M Foroutan","year":"2017","unstructured":"Foroutan, M., Cursons, J., Hediyeh-Zadeh, S., Thompson, E. W. & Davis, M. J. A Transcriptional Program for Detecting TGFbeta-Induced EMT in Cancer. Molecular cancer research: MCR 15, 619\u2013631, https:\/\/doi.org\/10.1158\/1541-7786.MCR-16-0313 (2017).","journal-title":"Molecular cancer research: MCR"},{"key":"37101_CR53","first-page":"2173","volume":"34","author":"L Minafra","year":"2014","unstructured":"Minafra, L. et al. Gene expression profiling of epithelial-mesenchymal transition in primary breast cancer cell culture. Anticancer research 34, 2173\u20132183 (2014).","journal-title":"Anticancer research"},{"key":"37101_CR54","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1177\/089686080502500110","volume":"25","author":"H Noh","year":"2005","unstructured":"Noh, H. et al. Angiotensin II mediates high glucose-induced TGF-beta1 and fibronectin upregulation in HPMC through reactive oxygen species. Peritoneal dialysis international: journal of the International Society for Peritoneal Dialysis 25, 38\u201347 (2005).","journal-title":"Peritoneal dialysis international: journal of the International Society for Peritoneal Dialysis"},{"key":"37101_CR55","doi-asserted-by":"publisher","first-page":"3448","DOI":"10.1093\/bioinformatics\/bti551","volume":"21","author":"S Maere","year":"2005","unstructured":"Maere, S., Heymans, K. & Kuiper, M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448\u20133449, https:\/\/doi.org\/10.1093\/bioinformatics\/bti551 (2005).","journal-title":"Bioinformatics"},{"key":"37101_CR56","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1210\/me.2009-0391","volume":"24","author":"CE Hills","year":"2010","unstructured":"Hills, C. E., Willars, G. B. & Brunskill, N. J. Proinsulin C-peptide antagonizes the profibrotic effects of TGF-beta1 via up-regulation of retinoic acid and HGF-related signaling pathways. Molecular endocrinology 24, 822\u2013831, https:\/\/doi.org\/10.1210\/me.2009-0391 (2010).","journal-title":"Molecular endocrinology"},{"key":"37101_CR57","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1093\/bioinformatics\/btp683","volume":"26","author":"MA Sartor","year":"2010","unstructured":"Sartor, M. A. et al. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics 26, 456\u2013463, https:\/\/doi.org\/10.1093\/bioinformatics\/btp683 (2010).","journal-title":"Bioinformatics"},{"key":"37101_CR58","doi-asserted-by":"publisher","first-page":"e13002","DOI":"10.1371\/journal.pone.0013002","volume":"5","author":"KA Maupin","year":"2010","unstructured":"Maupin, K. A. et al. Glycogene expression alterations associated with pancreatic cancer epithelial-mesenchymal transition in complementary model systems. PloS one 5, e13002, https:\/\/doi.org\/10.1371\/journal.pone.0013002 (2010).","journal-title":"PloS one"},{"key":"37101_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-3-73","volume":"3","author":"H Qin","year":"2009","unstructured":"Qin, H. et al. An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. BMC systems biology 3, 73, https:\/\/doi.org\/10.1186\/1752-0509-3-73 (2009).","journal-title":"BMC systems biology"},{"key":"37101_CR60","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1021\/pr060326s","volume":"6","author":"YM Kim","year":"2007","unstructured":"Kim, Y. M., Song, E. J., Seo, J., Kim, H. J. & Lee, K. J. Proteomic analysis of tyrosine phosphorylations in vascular endothelial growth factor- and reactive oxygen species-mediated signaling pathway. Journal of proteome research 6, 593\u2013601, https:\/\/doi.org\/10.1021\/pr060326s (2007).","journal-title":"Journal of proteome research"},{"key":"37101_CR61","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-2","volume":"4","author":"GD Bader","year":"2003","unstructured":"Bader, G. D. & Hogue, C. W. An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics 4, 2 (2003).","journal-title":"BMC bioinformatics"},{"key":"37101_CR62","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-3-86","volume":"3","author":"O Atias","year":"2009","unstructured":"Atias, O., Chor, B. & Chamovitz, D. A. Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. BMC systems biology 3, 86, https:\/\/doi.org\/10.1186\/1752-0509-3-86 (2009).","journal-title":"BMC systems biology"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-37101-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-37101-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-37101-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T05:35:13Z","timestamp":1671255313000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-018-37101-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,2,6]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["37101"],"URL":"https:\/\/doi.org\/10.1038\/s41598-018-37101-9","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,2,6]]},"assertion":[{"value":"25 July 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 November 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 February 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"1497"}}