{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T06:00:20Z","timestamp":1768284020783,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2016,12,27]],"date-time":"2016-12-27T00:00:00Z","timestamp":1482796800000},"content-version":"vor","delay-in-days":361,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,1]]},"abstract":"<jats:p>Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed\/used in a specified set of cells\/tissues, based on the use of interactive sliders. With the help of sliders, SlideBase enables users to define custom expression thresholds for individual cell types\/tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS.<\/jats:p>\n               <jats:p>Database URL: http:\/\/slidebase.binf.ku.dk<\/jats:p>","DOI":"10.1093\/database\/baw144","type":"journal-article","created":{"date-parts":[[2016,10,18]],"date-time":"2016-10-18T16:17:23Z","timestamp":1476807443000},"source":"Crossref","is-referenced-by-count":25,"title":["On-the-fly selection of cell-specific enhancers, genes, miRNAs and\n                    proteins across the human body using SlideBase"],"prefix":"10.1093","volume":"2016","author":[{"given":"Hans","family":"Ienasescu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kang","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robin","family":"Andersson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morana","family":"Vitezic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Rennie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristoffer","family":"Vitting-Seerup","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emil","family":"Lagoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mette","family":"Boyd","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jette","family":"Bornholdt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michiel J. L.","family":"de Hoon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hideya","family":"Kawaji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timo","family":"Lassmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"The FANTOM Consortium","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoshihide","family":"Hayashizaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alistair R. R.","family":"Forrest","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piero","family":"Carninci","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Albin","family":"Sandelin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,12,26]]},"reference":[{"key":"2019081505045931400_baw144-B1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2019081505045931400_baw144-B2","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Proteomics. Tissue-based map of the human proteome","volume":"347","author":"Uhl\u00e9n","year":"2015","journal-title":"Science"},{"key":"2019081505045931400_baw144-B3","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/nature13182","article-title":"A promoter-level mammalian expression atlas","volume":"507","author":"Forrest","year":"2014","journal-title":"Nature"},{"key":"2019081505045931400_baw144-B4","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1126\/science.aaa0355","article-title":"Human genomics. The human transcriptome across tissues and individuals","volume":"348","author":"Mel\u00e9","year":"2015","journal-title":"Science"},{"key":"2019081505045931400_baw144-B5","doi-asserted-by":"crossref","first-page":"D917","DOI":"10.1093\/nar\/gkv1101","article-title":"BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis","volume":"44","author":"Bagger","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B6","doi-asserted-by":"crossref","first-page":"D746","DOI":"10.1093\/nar\/gkv1045","article-title":"Expression Atlas update\u2014an integrated database of gene and protein expression in humans, animals and plants","volume":"44","author":"Petryszak","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B7","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gks1114","article-title":"BioGPS and MyGene.info: organizing online, gene-centric information","volume":"41","author":"Wu","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B8","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1101\/gr.084541.108","article-title":"Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE","volume":"19","author":"Valen","year":"2008","journal-title":"Genome Res"},{"key":"2019081505045931400_baw144-B9","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature12787","article-title":"An atlas of active enhancers across human cell types and tissues","volume":"507","author":"Andersson","year":"2014","journal-title":"Nature"},{"key":"2019081505045931400_baw144-B10","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s13059-014-0560-6","article-title":"Gateways to the FANTOM5 promoter level mammalian expression atlas","volume":"16","author":"Lizio","year":"2015","journal-title":"Genome Biol"},{"key":"2019081505045931400_baw144-B11","doi-asserted-by":"crossref","first-page":"D717","DOI":"10.1093\/nar\/gkv1275","article-title":"The UCSC Genome Browser database: 2016 update","volume":"44","author":"Speir","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B12","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nbt.2840","article-title":"Interactive visualization and analysis of large-scale sequencing datasets using ZENBU","volume":"32","author":"Severin","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2019081505045931400_baw144-B13","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B14","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B15","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1126\/science.1259418","article-title":"Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells","volume":"347","author":"Arner","year":"2015","journal-title":"Science"},{"key":"2019081505045931400_baw144-B16","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gku1055","article-title":"Gene: a gene-centered information resource at NCBI","volume":"43","author":"Brown","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B17","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","author":"UniProt Consortium","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2019081505045931400_baw144-B18","doi-asserted-by":"crossref","first-page":"W724","DOI":"10.1093\/nar\/gkq503","article-title":"Opal web services for biomedical applications","volume":"38","author":"Ren","year":"2010","journal-title":"Nucleic Acids Res"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baw144\/29164426\/baw144.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,16]],"date-time":"2019-08-16T12:16:21Z","timestamp":1565957781000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baw144\/2742072"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,1]]},"references-count":18,"URL":"https:\/\/doi.org\/10.1093\/database\/baw144","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2016,1]]},"published":{"date-parts":[[2016,1,1]]},"article-number":"baw144"}}