{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T20:50:19Z","timestamp":1775422219096,"version":"3.50.1"},"reference-count":32,"publisher":"Proceedings of the National Academy of Sciences","issue":"6","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2003,3,18]]},"abstract":"<jats:p>\n            We propose\n            <jats:sc>motif regressor<\/jats:sc>\n            for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity.\n            <jats:sc>motif regressor<\/jats:sc>\n            is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions. When applied to\n            <jats:italic>Saccharomyces cerevisiae<\/jats:italic>\n            ,\n            <jats:sc>motif regressor<\/jats:sc>\n            identified the ROX1 and YAP1 motifs from Rox1p and Yap1p overexpression experiments, respectively; predicted that Gcn4p may have increased activity in\n            <jats:italic>YAP1<\/jats:italic>\n            deletion mutants; reported a group of motifs (including GCN4, PHO4, MET4, STRE, USR1, RAP1, M3A, and M3B) that may mediate the transcriptional response to amino acid starvation; and found all of the known cell-cycle regulation motifs from 18 expression microarrays over two cell cycles.\n          <\/jats:p>","DOI":"10.1073\/pnas.0630591100","type":"journal-article","created":{"date-parts":[[2003,3,18]],"date-time":"2003-03-18T23:15:05Z","timestamp":1048029305000},"page":"3339-3344","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":237,"title":["Integrating regulatory motif discovery and genome-wide expression analysis"],"prefix":"10.1073","volume":"100","author":[{"given":"Erin M.","family":"Conlon","sequence":"first","affiliation":[{"name":"Department of Statistics, Harvard University, Cambridge, MA 02138; Department of Biostatistics, Harvard School of Public Health, Dana Farber Cancer Institute, Boston, MA 02115; and Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, NC 27599"}]},{"given":"X. Shirley","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University, Cambridge, MA 02138; Department of Biostatistics, Harvard School of Public Health, Dana Farber Cancer Institute, Boston, MA 02115; and Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, NC 27599"}]},{"given":"Jason D.","family":"Lieb","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University, Cambridge, MA 02138; Department of Biostatistics, Harvard School of Public Health, Dana Farber Cancer Institute, Boston, MA 02115; and Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, NC 27599"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University, Cambridge, MA 02138; Department of Biostatistics, Harvard School of Public Health, Dana Farber Cancer Institute, Boston, MA 02115; and Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, NC 27599"}]}],"member":"341","published-online":{"date-parts":[[2003,3,7]]},"reference":[{"key":"e_1_3_3_1_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.1947"},{"key":"e_1_3_3_2_2","first-page":"384","volume":"8","author":"Vilo J","year":"2000","unstructured":"J Vilo, A Brazma, I Jonassen, A Robinson, E Ukkonen Proc Int Conf Intell Syst Mol Biol 8, 384\u2013394 (2000).","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"e_1_3_3_3_2","first-page":"344","volume":"8","author":"Sinha S","year":"2000","unstructured":"S Sinha, M Tompa Proc Int Conf Intell Syst Mol Biol 8, 344\u2013354 (2000).","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.4.513"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.8211139"},{"key":"e_1_3_3_6_2","first-page":"303","volume":"12","author":"Grundy W N","year":"1996","unstructured":"W N Grundy, T L Bailey, C P Elkan Comput Appl Biosci 12, 303\u2013310 (1996).","journal-title":"Comput Appl Biosci"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.86.4.1183"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.180265397"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1098-939"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3519"},{"key":"e_1_3_3_11_2","first-page":"202","volume":"8","author":"Holmes I","year":"2000","unstructured":"I Holmes, W J Bruno Proc Int Conf Intell Syst Mol Biol 8, 202\u2013210 (2000).","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/84792"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.9.1167"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt717"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.12.10.2987"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.11.12.4241"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/77116"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.9.12.3273"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1075090"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng907"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/15.7.607"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.17.12.6982"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/18.20.6097"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/10343"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/17.21.6327"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.11.12.4309"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng569"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0968-0004(99)01460-7"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.17.7.3536"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.25.14863"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(01)00494-9"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.16.6.2830"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.0630591100","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T19:25:12Z","timestamp":1649791512000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.0630591100"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,3,7]]},"references-count":32,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2003,3,18]]}},"alternative-id":["10.1073\/pnas.0630591100"],"URL":"https:\/\/doi.org\/10.1073\/pnas.0630591100","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2003,3,7]]},"assertion":[{"value":"2002-12-11","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2003-01-30","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2003-03-07","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}