Identification of O-glycosylation related genes and subtypes in ulcerative colitis based on machine learning
Ulcerative colitis (UC) is an immune-related inflammatory bowel disease, with its underlying mechanisms being a central area of clinical research. O-GlcNAcylation plays a critical role in regulating immunity progression and the occurrence of inflammatory diseases and tumors. Yet, the mechanism of O-...
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| description | Ulcerative colitis (UC) is an immune-related inflammatory bowel disease, with its underlying mechanisms being a central area of clinical research. O-GlcNAcylation plays a critical role in regulating immunity progression and the occurrence of inflammatory diseases and tumors. Yet, the mechanism of O-GlcNAc-associated colitis remains to be elucidated. To this end, the transcriptional and clinical data of GSE75214 and GSE92415 from the GEO database was hereby examined, and genes MUC1, ADAMTS1, GXYLT2, and SEMA5A were found to be significantly related to O-GlcNAcylation using machine learning methods. Based on the four hub genes, two UC subtypes were built. Notably, subtype B might be prone to developing colitis-associated colorectal cancer (CAC). This study delved into the role of intestinal glycosylation changes, especially the O-GlcNAcylation, and forged a foundation for further research on the occurrence and development of UC. Overall, understanding the role of O-GlcNAcylation in UC could have significant implications for diagnosis and treatment, offering valuable insights into the disease's progression. |
| doi_str_mv | 10.1371/journal.pone.0311495 |
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O-GlcNAcylation plays a critical role in regulating immunity progression and the occurrence of inflammatory diseases and tumors. Yet, the mechanism of O-GlcNAc-associated colitis remains to be elucidated. To this end, the transcriptional and clinical data of GSE75214 and GSE92415 from the GEO database was hereby examined, and genes MUC1, ADAMTS1, GXYLT2, and SEMA5A were found to be significantly related to O-GlcNAcylation using machine learning methods. Based on the four hub genes, two UC subtypes were built. Notably, subtype B might be prone to developing colitis-associated colorectal cancer (CAC). This study delved into the role of intestinal glycosylation changes, especially the O-GlcNAcylation, and forged a foundation for further research on the occurrence and development of UC. Overall, understanding the role of O-GlcNAcylation in UC could have significant implications for diagnosis and treatment, offering valuable insights into the disease's progression.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0311495</identifier><identifier>PMID: 39739658</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>ADAMTS-1 protein ; Analysis ; Antigens ; Bioinformatics ; Biology and Life Sciences ; Colitis, Ulcerative - genetics ; Colitis, Ulcerative - metabolism ; Colorectal cancer ; Colorectal carcinoma ; Datasets ; Development and progression ; Disease ; Gene expression ; Genes ; Genetic aspects ; Glycosylation ; Health aspects ; Humans ; Inflammatory bowel disease ; Inflammatory bowel diseases ; Learning algorithms ; Machine Learning ; Medicine and Health Sciences ; Metabolism ; O-GlcNAcylation ; Pathogenesis ; Proteins ; Risk factors ; Software ; Support vector machines ; Transcription factors ; Ulcerative colitis</subject><ispartof>PloS one, 2024-12, Vol.19 (12), p.e0311495</ispartof><rights>Copyright: © 2024 Lu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2024 Public Library of Science</rights><rights>2024 Lu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 Lu et al 2024 Lu et al</rights><rights>2024 Lu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c4875-de7b37561dd795cfc87e707b59a6c0a5537f2c45dbc82d5c1318c9879db325d33</cites><orcidid>0009-0006-0310-4763</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11687659/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11687659/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39739658$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lu, Yue</creatorcontrib><creatorcontrib>Su, Yi</creatorcontrib><creatorcontrib>Wang, Nan</creatorcontrib><creatorcontrib>Li, Dongyue</creatorcontrib><creatorcontrib>Zhang, Huichao</creatorcontrib><creatorcontrib>Xu, Hongyu</creatorcontrib><title>Identification of O-glycosylation related genes and subtypes in ulcerative colitis based on machine learning</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Ulcerative colitis (UC) is an immune-related inflammatory bowel disease, with its underlying mechanisms being a central area of clinical research. O-GlcNAcylation plays a critical role in regulating immunity progression and the occurrence of inflammatory diseases and tumors. Yet, the mechanism of O-GlcNAc-associated colitis remains to be elucidated. To this end, the transcriptional and clinical data of GSE75214 and GSE92415 from the GEO database was hereby examined, and genes MUC1, ADAMTS1, GXYLT2, and SEMA5A were found to be significantly related to O-GlcNAcylation using machine learning methods. Based on the four hub genes, two UC subtypes were built. Notably, subtype B might be prone to developing colitis-associated colorectal cancer (CAC). This study delved into the role of intestinal glycosylation changes, especially the O-GlcNAcylation, and forged a foundation for further research on the occurrence and development of UC. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lu, Yue</au><au>Su, Yi</au><au>Wang, Nan</au><au>Li, Dongyue</au><au>Zhang, Huichao</au><au>Xu, Hongyu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of O-glycosylation related genes and subtypes in ulcerative colitis based on machine learning</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2024-12-31</date><risdate>2024</risdate><volume>19</volume><issue>12</issue><spage>e0311495</spage><pages>e0311495-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Ulcerative colitis (UC) is an immune-related inflammatory bowel disease, with its underlying mechanisms being a central area of clinical research. O-GlcNAcylation plays a critical role in regulating immunity progression and the occurrence of inflammatory diseases and tumors. Yet, the mechanism of O-GlcNAc-associated colitis remains to be elucidated. To this end, the transcriptional and clinical data of GSE75214 and GSE92415 from the GEO database was hereby examined, and genes MUC1, ADAMTS1, GXYLT2, and SEMA5A were found to be significantly related to O-GlcNAcylation using machine learning methods. Based on the four hub genes, two UC subtypes were built. Notably, subtype B might be prone to developing colitis-associated colorectal cancer (CAC). This study delved into the role of intestinal glycosylation changes, especially the O-GlcNAcylation, and forged a foundation for further research on the occurrence and development of UC. Overall, understanding the role of O-GlcNAcylation in UC could have significant implications for diagnosis and treatment, offering valuable insights into the disease's progression.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>39739658</pmid><doi>10.1371/journal.pone.0311495</doi><tpages>e0311495</tpages><orcidid>https://orcid.org/0009-0006-0310-4763</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | ADAMTS-1 protein Analysis Antigens Bioinformatics Biology and Life Sciences Colitis, Ulcerative - genetics Colitis, Ulcerative - metabolism Colorectal cancer Colorectal carcinoma Datasets Development and progression Disease Gene expression Genes Genetic aspects Glycosylation Health aspects Humans Inflammatory bowel disease Inflammatory bowel diseases Learning algorithms Machine Learning Medicine and Health Sciences Metabolism O-GlcNAcylation Pathogenesis Proteins Risk factors Software Support vector machines Transcription factors Ulcerative colitis |
| title | Identification of O-glycosylation related genes and subtypes in ulcerative colitis based on machine learning |
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