{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T15:10:27Z","timestamp":1768489827941,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,16]],"date-time":"2019-11-16T00:00:00Z","timestamp":1573862400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41HD064556"],"award-info":[{"award-number":["P41HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["RRID:SCR 007164"],"award-info":[{"award-number":["RRID:SCR 007164"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated \u2018gene expression as a phenotype\u2019 and gene regulatory network analyses.<\/jats:p>","DOI":"10.1093\/nar\/gkz933","type":"journal-article","created":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T20:09:15Z","timestamp":1573589355000},"source":"Crossref","is-referenced-by-count":30,"title":["Xenbase: deep integration of GEO &amp; SRA RNA-seq and ChIP-seq data in a model organism database"],"prefix":"10.1093","author":[{"given":"Joshua D","family":"Fortriede","sequence":"first","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Troy J","family":"Pells","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]},{"given":"Stanley","family":"Chu","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]},{"given":"Praneet","family":"Chaturvedi","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"DongZhuo","family":"Wang","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]},{"given":"Malcom E","family":"Fisher","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Christina","family":"James-Zorn","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]},{"given":"Ying","family":"Wang","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Mardi J","family":"Nenni","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Kevin A","family":"Burns","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Vaneet S","family":"Lotay","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]},{"given":"Virgilio G","family":"Ponferrada","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Kamran","family":"Karimi","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]},{"given":"Aaron M","family":"Zorn","sequence":"additional","affiliation":[{"name":"Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA"}]},{"given":"Peter D","family":"Vize","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,11,16]]},"reference":[{"key":"2019111604501807500_B1","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.ydbio.2019.03.015","article-title":"A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis","volume":"452","author":"Mitros","year":"2019","journal-title":"Dev. Biol."},{"key":"2019111604501807500_B2","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/nature19840","article-title":"Genome evolution in the allotetraploid frog Xenopus laevis","volume":"538","author":"Session","year":"2016","journal-title":"Nature"},{"key":"2019111604501807500_B3","doi-asserted-by":"crossref","first-page":"D861","DOI":"10.1093\/nar\/gkx936","article-title":"Xenbase: a genomic, epigenomic and transcriptomic model organism database","volume":"46","author":"Karimi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019111604501807500_B4","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/978-1-4939-7737-6_10","article-title":"Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database","volume":"1757","author":"James-Zorn","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"2019111604501807500_B5","doi-asserted-by":"crossref","first-page":"154","DOI":"10.3389\/fphys.2019.00154","article-title":"Xenbase: facilitating the use of Xenopus to model human disease","volume":"10","author":"Nenni","year":"2019","journal-title":"Front. Physiol."},{"key":"2019111604501807500_B6","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2013update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2019111604501807500_B7","doi-asserted-by":"crossref","first-page":"D794","DOI":"10.1093\/nar\/gkx1081","article-title":"The Encyclopedia of DNA elements (ENCODE): data portal update","volume":"46","author":"Davies","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019111604501807500_B8","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/2041-1480-4-31","article-title":"Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase","volume":"4","author":"Segerdell","year":"2013","journal-title":"J. Biomed. Semantics"},{"key":"2019111604501807500_B9","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2019111604501807500_B10","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2019111604501807500_B11","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"2019111604501807500_B12","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2019111604501807500_B13","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1038\/nbt.2931","article-title":"Normalization of RNA-Seq data using factor analysis of control genes or samples","volume":"32","author":"Risso","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2019111604501807500_B14","doi-asserted-by":"crossref","first-page":"W187","DOI":"10.1093\/nar\/gku365","article-title":"deepTools: a flexible platform for exploring deep-sequencing data","volume":"42","author":"Ramirez","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2019111604501807500_B15","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz933\/30857989\/gkz933.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz933\/30857989\/gkz933.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,16]],"date-time":"2019-11-16T09:50:32Z","timestamp":1573897832000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkz933\/5626530"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,16]]},"references-count":15,"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz933","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,16]]},"article-number":"gkz933"}}