{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T19:13:06Z","timestamp":1767985986277,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,7,15]],"date-time":"2021-07-15T00:00:00Z","timestamp":1626307200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","award":["NRF-NRFF2012-054"],"award-info":[{"award-number":["NRF-NRFF2012-054"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"name":"RNA Biology Center at the Cancer Science Institute of Singapore"},{"name":"Singapore Ministry of Education Academic Research Fund Tier 3","award":["MOE2014-T3-1-006"],"award-info":[{"award-number":["MOE2014-T3-1-006"]}]},{"name":"National Research Foundation Competitive Research Programme","award":["NRF-CRP17-2017-02"],"award-info":[{"award-number":["NRF-CRP17-2017-02"]}]},{"DOI":"10.13039\/501100001475","name":"Nanyang Technological University","doi-asserted-by":"publisher","award":["NTU-ACE2019-03"],"award-info":[{"award-number":["NTU-ACE2019-03"]}],"id":[{"id":"10.13039\/501100001475","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Epigenomics and transcriptomics data from high-throughput sequencing techniques such as RNA-seq and ChIP-seq have been successfully applied in predicting gene transcript expression. However, the locations of chromatin loops in the genome identified by techniques such as Chromatin Interaction Analysis with Paired End Tag sequencing (ChIA-PET) have never been used for prediction tasks. Here, we developed machine learning models to investigate if ChIA-PET could contribute to transcript and exon usage prediction. In doing so, we used a large set of transcription factors as well as ChIA-PET data. We developed different Gradient Boosting Trees models according to the different tasks with the integrated datasets from three cell lines, including GM12878, HeLaS3 and K562. We validated the models via 10-fold cross validation, chromosome-split validation and cross-cell validation. Our results show that both transcript and splicing-derived exon usage can be effectively predicted with at least 0.7512 and 0.7459 of accuracy, respectively, on all cell lines from all kinds of validations. Examining the predictive features, we found that RNA Polymerase II ChIA-PET was one of the most important features in both transcript and exon usage prediction, suggesting that chromatin loop anchors are predictive of both transcript and exon usage.<\/jats:p>","DOI":"10.1093\/bib\/bbab254","type":"journal-article","created":{"date-parts":[[2021,6,17]],"date-time":"2021-06-17T19:10:09Z","timestamp":1623957009000},"source":"Crossref","is-referenced-by-count":5,"title":["Chromatin loop anchors predict transcript and exon usage"],"prefix":"10.1093","volume":"22","author":[{"given":"Yu","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yichao","family":"Cai","sequence":"additional","affiliation":[{"name":"Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xavier","family":"Roca","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chee Keong","family":"Kwoh","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa Jane","family":"Fullwood","sequence":"additional","affiliation":[{"name":"Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore"},{"name":"School of Biological Sciences, Nanyang Technological University, 637551, Singapore"},{"name":"Institute of Molecular and Cell Biology, Agency for Science, Technology and Research 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