{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T00:58:18Z","timestamp":1772499498729,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009773","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T00:00:00Z","timestamp":1655424000000}}],"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T00:00:00Z","timestamp":1654560000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31902231"],"award-info":[{"award-number":["31902231"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31402055"],"award-info":[{"award-number":["31402055"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"College Students' Innovation and Entrepreneurship Training Program of Yangtze University","award":["2020084"],"award-info":[{"award-number":["2020084"]}]},{"name":"Teaching research project of Yangtze University","award":["JY2020125"],"award-info":[{"award-number":["JY2020125"]}]},{"name":"Graduate Teaching Program of Yangtze University","award":["YAL202108"],"award-info":[{"award-number":["YAL202108"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Transcription factor (TF) regulates the transcription of DNA to messenger RNA by binding to upstream sequence motifs. Identifying the locations of known motifs in whole genomes is computationally intensive.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methodology\/Principal findings<\/jats:title>\n                    <jats:p>\n                      This study presents a computational tool, named \u201cGrit\u201d, for screening TF-binding sites (TFBS) by coordinating transcription factors to their promoter sequences in orthologous genes. This tool employs a newly developed mixed Student\u2019s\n                      <jats:italic>t<\/jats:italic>\n                      -test statistical method that detects high-scoring binding sites utilizing conservation information among species. The program performs sequence scanning at a rate of 3.2 Mbp\/s on a quad-core Amazon server and has been benchmarked by the well-established ChIP-Seq datasets, putting Grit amongst the top-ranked TFBS predictors. It significantly outperforms the well-known transcription factor motif scanning tools, Pscan (4.8%) and FIMO (17.8%), in analyzing well-documented ChIP-Atlas human genome Chip-Seq datasets.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Significance<\/jats:title>\n                    <jats:p>Grit is a good alternative to current available motif scanning tools.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pcbi.1009773","type":"journal-article","created":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T13:32:56Z","timestamp":1654608776000},"page":"e1009773","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["Identification of upstream transcription factor binding sites in orthologous genes using mixed Student\u2019s t-test 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