{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T01:30:07Z","timestamp":1772069407694,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T00:00:00Z","timestamp":1688083200000},"content-version":"vor","delay-in-days":180,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AG074549 CA217078 CA223662 MD011439 NS115403"],"award-info":[{"award-number":["AG074549 CA217078 CA223662 MD011439 NS115403"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AG074549 CA217078 CA223662 MD011439 NS115403"],"award-info":[{"award-number":["AG074549 CA217078 CA223662 MD011439 NS115403"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Epigenetic modifications play critical roles in gene regulation and disease pathobiology. Highly sensitive enabling technologies, including microarray- and sequencing-based approaches have allowed genome-wide profiling of cytosine modifications in DNAs in clinical samples to facilitate discovery of epigenetic biomarkers for disease diagnosis and prognosis. Historically, many previous studies, however, did not distinguish the most investigated 5-methylcytosines (5mC) from other modified cytosines, especially the biochemically stable\u00a05-hydroxymethylcytosines (5hmC), which have been shown to have a distinct genomic distribution and regulatory role from 5mC. Notably, during the past several years, the 5hmC-Seal, a highly sensitive chemical labeling technique, has been demonstrated to be a powerful tool for genome-wide profiling of 5hmC in clinically feasible biospecimens (e.g. a few milliliter of plasma or serum). The 5hmC-Seal technique has been utilized by our team in biomarker discovery for human cancers and other complex diseases using circulating cell-free DNA (cfDNA), as well as the characterization of the first 5hmC Human Tissue Map. Convenient access to the accumulating 5hmC-Seal data will allow the research community to validate and re-use these results, potentially providing novel insights into epigenetic contribution to a range of human diseases. Here we introduce the PETCH-DB, an integrated database that was implemented to provide 5hmC-related results generated using the 5hmC-Seal technique. We aim the PETCH-DB to be a central portal, which will be available to the scientific community with regularly updated 5hmC data in clinical samples to reflect current advances in this field.<\/jats:p><jats:p>Database URL http:\/\/petch-db.org\/<\/jats:p>","DOI":"10.1093\/database\/baad042","type":"journal-article","created":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T10:04:56Z","timestamp":1688119496000},"source":"Crossref","is-referenced-by-count":7,"title":["PETCH-DB: a Portal for\u00a0Exploring Tissue-specific and\u00a0Complex disease-associated 5-Hydroxymethylcytosines"],"prefix":"10.1093","volume":"2023","author":[{"given":"Qinyun","family":"Cai","sequence":"first","affiliation":[{"name":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , 680 N. Lake Shore Dr., Chicago, IL 60611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhou","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , 680 N. Lake Shore Dr., Chicago, IL 60611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaolong","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Chicago , 5735 S. Ellis Ave., Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang","family":"Zeng","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , 680 N. Lake Shore Dr., Chicago, IL 60611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiabin","family":"Cai","sequence":"additional","affiliation":[{"name":"Zhongshan Hospital, Fudan University , 180 Fenglin Rd., Shanghai 200032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiajun","family":"Cai","sequence":"additional","affiliation":[{"name":"Huashan Hospital, Fudan University , 12 Wulumuqi Rd., Shanghai 200040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University , 1 Jianshedong Rd., Zhengzhou, Henan Province 450052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Illinois , 808 S. Wood St., Chicago, IL 60612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixiang","family":"Shi","sequence":"additional","affiliation":[{"name":"Bionova (Shanghai) Medical Technology Co., Ltd. , Building 42, 100 Banxia Rd., Shanghai 201318, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zoe","family":"Arvanitakis","sequence":"additional","affiliation":[{"name":"Rush Alzheimer\u2019s Disease Center, Rush University Medical Center , 1620 W. Harrison St., Chicago,\u2009IL\u200960612,\u2009 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc A","family":"Bissonnette","sequence":"additional","affiliation":[{"name":"Department of Medicine, The University of Chicago , 5841 S. Maryland Ave., Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian C -H","family":"Chiu","sequence":"additional","affiliation":[{"name":"Department of Public Health Sciences, The University of Chicago , 5841 S. Maryland Ave., Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shi-Yuan","family":"Cheng","sequence":"additional","affiliation":[{"name":"The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine , 303 E. Superior St., Chicago, IL 60611, USA"},{"name":"The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine , 303 E. Superior St., Chicago, IL 60611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuan","family":"He","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Chicago , 5735 S. Ellis Ave., Chicago, IL 60637, USA"},{"name":"The Howard Hughes Medical Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0875-263X","authenticated-orcid":false,"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Northwestern University Feinberg School of Medicine , 680 N. Lake Shore Dr., Chicago, IL 60611, USA"},{"name":"The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine , 303 E. Superior St., Chicago, IL 60611, USA"},{"name":"Department of Chemistry, The University of Chicago , 5735 S. Ellis Ave., Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,6,10]]},"reference":[{"key":"2023063014165535400_R1","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nrg3080","article-title":"Uncovering the role of\u00a05-hydroxymethylcytosine in\u00a0the epigenome","volume":"13","author":"Branco","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023063014165535400_R2","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1038\/cr.2017.121","article-title":"5-Hydroxymethylcytosine signatures in\u00a0circulating cell-free DNA as diagnostic biomarkers for\u00a0human cancers","volume":"27","author":"Li","year":"2017","journal-title":"Cell Res."},{"key":"2023063014165535400_R3","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-20001-w","article-title":"A human tissue map of\u00a05-hydroxymethylcytosines exhibits tissue specificity through gene and\u00a0enhancer modulation","volume":"11","author":"Cui","year":"2020","journal-title":"Nat. Commun."},{"key":"2023063014165535400_R4","doi-asserted-by":"crossref","DOI":"10.1186\/s40880-019-0356-x","article-title":"Towards precision medicine: advances in\u00a05-hydroxymethylcytosine cancer biomarker discovery in\u00a0liquid biopsy","volume":"39","author":"Zeng","year":"2019","journal-title":"Cancer Commun."},{"key":"2023063014165535400_R5","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1373\/clinchem.2019.305508","article-title":"5-Hydroxymethylcytosines in\u00a0circulating cell-free DNA reveal vascular complications of\u00a0type 2 diabetes","volume":"65","author":"Yang","year":"2019","journal-title":"Clin. Chem."},{"key":"2023063014165535400_R6","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ygeno.2020.11.014","article-title":"Alterations of\u00a05-hydroxymethylcytosines in\u00a0circulating cell-free DNA reflect retinopathy in\u00a0type 2 diabetes","volume":"113","author":"Han","year":"2021","journal-title":"Genomics"},{"key":"2023063014165535400_R7","first-page":"49","article-title":"Genome-wide analysis reflects novel 5-hydroxymethylcytosines implicated in\u00a0diabetic nephropathy and\u00a0the biomarker potential","volume":"3","author":"Yang","year":"2022","journal-title":"Extracell. Vesicles Circulating Nucleic Acids"},{"key":"2023063014165535400_R8","doi-asserted-by":"crossref","DOI":"10.1002\/alz.076673","article-title":"A 5-hydroxymethylation-based clock derived cell-free DNA in blood reveals accelerated epigenetic aging in patients with Alzheimer's disease.","author":"Zhang","year":"2023"},{"key":"2023063014165535400_R9","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nbt.1732","article-title":"Selective chemical labeling reveals the genome-wide distribution of\u00a05-hydroxymethylcytosine","volume":"29","author":"Song","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2023063014165535400_R10","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/j.molcel.2016.06.028","article-title":"A highly sensitive and\u00a0robust method for\u00a0genome-wide 5hmC profiling of\u00a0rare cell populations","volume":"63","author":"Han","year":"2016","journal-title":"Mol. Cell"},{"key":"2023063014165535400_R11","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1136\/gutjnl-2019-318882","article-title":"Genome-wide mapping of\u00a05-hydroxymethylcytosines in\u00a0circulating cell-free DNA as a non-invasive approach for\u00a0early detection of\u00a0hepatocellular carcinoma","volume":"68","author":"Cai","year":"2019","journal-title":"Gut"},{"key":"2023063014165535400_R12","article-title":"An integrative analysis of\u00a0genome-wide 5-hydroxymethylcytosines in\u00a0circulating cell-free DNA detects noninvasive diagnostic markers for\u00a0gliomas","volume":"3","author":"Cai","year":"2021","journal-title":"Neurooncol. Adv."},{"key":"2023063014165535400_R13","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1182\/bloodadvances.2019000175","article-title":"Prognostic implications of\u00a05-hydroxymethylcytosines from circulating cell-free DNA in\u00a0diffuse large B-cell lymphoma","volume":"3","author":"Chiu","year":"2019","journal-title":"Blood Adv."},{"key":"2023063014165535400_R14","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baq020","article-title":"GeneCards Version 3: the human gene integrator","volume":"2010","author":"Safran","year":"2010","journal-title":"Database (Oxford)"},{"key":"2023063014165535400_R15","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for\u00a0the ENCODE project","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res."},{"key":"2023063014165535400_R16","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of\u00a0fold change and\u00a0dispersion for\u00a0RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"2023063014165535400_R17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/cpbi.5","article-title":"The GeneCards suite: from gene data mining to disease genome sequence analyses","volume":"54","author":"Stelzer","year":"2016","journal-title":"Curr. Protoc. Bioinform."},{"key":"2023063014165535400_R18","doi-asserted-by":"crossref","DOI":"10.3233\/JAD-221113","article-title":"Genome-wide mapping implicates 5-hydroxymethylcytosines in\u00a0diabetes mellitus and\u00a0Alzheimer\u2019s disease","author":"Beadell","year":"2023","journal-title":"J. Alzheimer\u2019s Dis."},{"key":"2023063014165535400_R19","doi-asserted-by":"crossref","DOI":"10.1038\/s41525-021-00179-8","article-title":"Alterations of\u00a05-hydroxymethylation in\u00a0circulating cell-free DNA reflect molecular distinctions of\u00a0subtypes of\u00a0non-Hodgkin lymphoma","volume":"6","author":"Chiu","year":"2021","journal-title":"NPJ. Genom. Med."},{"key":"2023063014165535400_R20","doi-asserted-by":"crossref","DOI":"10.1186\/s13045-022-01327-y","article-title":"Genome-wide profiling of\u00a05-hydroxymethylcytosines in\u00a0circulating cell-free DNA reveals population-specific pathways in\u00a0the development of\u00a0multiple myeloma","volume":"15","author":"Chiu","year":"2022","journal-title":"J. Hematol. Oncol."},{"key":"2023063014165535400_R21","doi-asserted-by":"crossref","DOI":"10.1186\/s13148-020-0810-2","article-title":"5-Hydroxymethylcytosine signatures in\u00a0circulating cell-free DNA as diagnostic and\u00a0predictive biomarkers for\u00a0coronary artery disease","volume":"12","author":"Dong","year":"2020","journal-title":"Clin Epigenetics"},{"key":"2023063014165535400_R22","first-page":"10","article-title":"Considerations before the application of\u00a05-hydroxymethylation levels of\u00a0long non-coding RNAs for\u00a0non-invasive cancer diagnosis","volume":"3","author":"Zhang","year":"2022","journal-title":"Extracell. Vesicles Circulating Nucleic Acids"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad042\/50758172\/baad042.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad042\/50758172\/baad042.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T03:22:39Z","timestamp":1729480959000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baad042\/7193833"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,1]]},"references-count":22,"URL":"https:\/\/doi.org\/10.1093\/database\/baad042","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2023,1,1]]},"article-number":"baad042"}}