{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T18:01:56Z","timestamp":1722880916681},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) or massive parallel sequencing (ChIP-seq) are enabling genome-wide identification of active promoters in different cellular conditions using antibodies against Pol-II. However, these methods produce enrichment not only near the gene promoters but also inside the genes and other genomic regions due to the non-specificity of the antibodies used in ChIP. Further, the use of these methods is limited by their high cost and strong dependence on cellular type and context.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>We trained and tested different state-of-art ensemble and meta classification methods for identification of Pol-II enriched promoter and Pol-II enriched non-promoter sequences, each of length 500 bp. The classification models were trained and tested on a bench-mark dataset, using a set of 39 different feature variables that are based on chromatin modification signatures and various DNA sequence features. The best performing model was applied on seven published ChIP-seq Pol-II datasets to provide genome wide annotation of mouse gene promoters.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We present a novel algorithm based on supervised learning methods to discriminate promoter associated Pol-II enrichment from enrichment elsewhere in the genome in ChIP-chip\/seq profiles. We accumulated a dataset of 11,773 promoter and 46,167 non-promoter sequences, each of length 500 bp, generated from RNA Pol-II ChIP-seq data of five tissues (Brain, Kidney, Liver, Lung and Spleen). We evaluated the classification models in building the best predictor and found that Bagging and Random Forest based approaches give the best accuracy. We implemented the algorithm on seven different published ChIP-seq datasets to provide a comprehensive set of promoter annotations for both protein-coding and non-coding genes in the mouse genome. The resulting annotations contain 13,413 (4,747) protein-coding (non-coding) genes with single promoters and 9,929 (1,858) protein-coding (non-coding) genes with two or more alternative promoters, and a significant number of unassigned novel promoters.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Our new algorithm can successfully predict the promoters from the genome wide profile of Pol-II bound regions. In addition, our algorithm performs significantly better than existing promoter prediction methods and can be applied for genome-wide predictions of Pol-II promoters.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-s1-s65","type":"journal-article","created":{"date-parts":[[2010,1,19]],"date-time":"2010-01-19T07:17:52Z","timestamp":1263885472000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data"],"prefix":"10.1186","volume":"11","author":[{"given":"Ravi","family":"Gupta","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priyankara","family":"Wikramasinghe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anirban","family":"Bhattacharyya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francisco A","family":"Perez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sharmistha","family":"Pal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramana V","family":"Davuluri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,1,18]]},"reference":[{"key":"4015_CR1","doi-asserted-by":"crossref","unstructured":"Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV: MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. Nucleic Acids Res 2006, (34 Database):D98\u2013103. 10.1093\/nar\/gkj096","DOI":"10.1093\/nar\/gkj096"},{"issue":"2","key":"4015_CR2","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1101\/gr.5872707","volume":"17","author":"D Baek","year":"2007","unstructured":"Baek D, Davis C, Ewing B, Gordon D, Green P: Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res 2007, 17(2):145\u2013155. 10.1101\/gr.5872707","journal-title":"Genome Res"},{"issue":"1","key":"4015_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1101\/gr.4222606","volume":"16","author":"SJ Cooper","year":"2006","unstructured":"Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM: Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res 2006, 16(1):1\u201310. 10.1101\/gr.4222606","journal-title":"Genome Res"},{"issue":"4","key":"4015_CR4","doi-asserted-by":"publisher","first-page":"R40","DOI":"10.1186\/gb-2009-10-4-r40","volume":"10","author":"H Kawaji","year":"2009","unstructured":"Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, et al.: The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biol 2009, 10(4):R40. 10.1186\/gb-2009-10-4-r40","journal-title":"Genome Biol"},{"issue":"4","key":"4015_CR5","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.tig.2008.01.008","volume":"24","author":"RV Davuluri","year":"2008","unstructured":"Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang TH: The functional consequences of alternative promoter use in mammalian genomes. Trends Genet 2008, 24(4):167\u2013177. 10.1016\/j.tig.2008.01.008","journal-title":"Trends Genet"},{"key":"4015_CR6","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1186\/1471-2164-9-349","volume":"9","author":"GA Singer","year":"2008","unstructured":"Singer GA, Wu J, Yan P, Plass C, Huang TH, Davuluri RV: Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics 2008, 9: 349. 10.1186\/1471-2164-9-349","journal-title":"BMC Genomics"},{"issue":"7052","key":"4015_CR7","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1038\/nature03877","volume":"436","author":"TH Kim","year":"2005","unstructured":"Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B: A high-resolution map of active promoters in the human genome. Nature 2005, 436(7052):876\u2013880. 10.1038\/nature03877","journal-title":"Nature"},{"issue":"4","key":"4015_CR8","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","volume":"129","author":"A Barski","year":"2007","unstructured":"Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K: High-resolution profiling of histone methylations in the human genome. Cell 2007, 129(4):823\u2013837. 10.1016\/j.cell.2007.05.009","journal-title":"Cell"},{"issue":"1","key":"4015_CR9","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1038\/nbt.1518","volume":"27","author":"J Rozowsky","year":"2009","unstructured":"Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 2009, 27(1):66\u201375. 10.1038\/nbt.1518","journal-title":"Nat Biotechnol"},{"issue":"5","key":"4015_CR10","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1016\/j.cell.2008.02.022","volume":"132","author":"DE Schones","year":"2008","unstructured":"Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K: Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132(5):887\u2013898. 10.1016\/j.cell.2008.02.022","journal-title":"Cell"},{"issue":"1","key":"4015_CR11","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1002\/jcb.22250","volume":"108","author":"BM Lee","year":"2009","unstructured":"Lee BM, Mahadevan LC: Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking. J Cell Biochem 2009, 108(1):22\u201334. 10.1002\/jcb.22250","journal-title":"J Cell Biochem"},{"key":"4015_CR12","unstructured":"UCSC Genome Browser[http:\/\/hgdownload.cse.ucsc.edu\/]"},{"key":"4015_CR13","unstructured":"Center for Systems & Computational Biology, The Wistar Institute[http:\/\/bioinfo.wistar.upenn.edu\/promoterprediction]"},{"key":"4015_CR14","unstructured":"WEKA data-mining toolbox[http:\/\/www.cs.waikato.ac.nz\/ml\/weka\/]"},{"key":"4015_CR15","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1214\/aos\/1016218223","volume":"28","author":"J Friedman","year":"1998","unstructured":"Friedman J, Hastie T, Tibshirani R: Additive logistic regression: a statistical view of boosting. Ann Stat 1998, 28: 337\u2013407. 10.1214\/aos\/1016218223","journal-title":"Ann Stat"},{"issue":"2","key":"4015_CR16","first-page":"123","volume":"24","author":"L Breiman","year":"1996","unstructured":"Breiman L: Bagging predictors. Mach Learn 1996, 24(2):123\u2013140.","journal-title":"Mach Learn"},{"issue":"10","key":"4015_CR17","doi-asserted-by":"publisher","first-page":"1619","DOI":"10.1109\/TPAMI.2006.211","volume":"28","author":"JJ Rodriguez","year":"2006","unstructured":"Rodriguez JJ, Alonso CJ, Kuncheva LI: Rotation Forest: A New Classifier Ensemble Method. IEEE Trans Pattern Anal Mach Intell 2006, 28(10):1619\u20131630. 10.1109\/TPAMI.2006.211","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"issue":"1","key":"4015_CR18","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman L: Random Forests. Mach Learn 2001, 45(1):5\u201332. 10.1023\/A:1010933404324","journal-title":"Mach Learn"},{"issue":"2","key":"4015_CR19","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1101\/gr.6991408","volume":"18","author":"T Abeel","year":"2008","unstructured":"Abeel T, Saeys Y, Bonnet E, Rouze P, Peer Y: Generic eukaryotic core promoter prediction using structural features of DNA. Genome Research 2008, 18(2):310\u2013323. 10.1101\/gr.6991408","journal-title":"Genome Research"},{"issue":"6","key":"4015_CR20","first-page":"1258","volume":"28","author":"VI Ivanov","year":"1994","unstructured":"Ivanov VI, Minchenkova LE: [The A-form of DNA: in search of the biological role]. Mol Biol (Mosk) 1994, 28(6):1258\u20131271.","journal-title":"Mol Biol (Mosk)"},{"issue":"10","key":"4015_CR21","doi-asserted-by":"publisher","first-page":"2341","DOI":"10.1002\/bip.1978.360171005","volume":"17","author":"RL Ornstein","year":"1978","unstructured":"Ornstein RL, Rein R, Breen DL, Macelroy RD: OPTIMIZED POTENTIAL FUNCTION FOR CALCULATION OF NUCLEIC-ACID INTERACTION ENERGIES .1. BASE STACKING. Biopolymers 1978, 17(10):2341\u20132360. 10.1002\/bip.1978.360171005","journal-title":"Biopolymers"},{"issue":"1","key":"4015_CR22","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1006\/jmbi.1994.0120","volume":"247","author":"AA Gorin","year":"1995","unstructured":"Gorin AA, Zhurkin VB, Olson WK: B-DNA twisting correlates with base-pair morphology. J Mol Biol 1995, 247(1):34\u201348. 10.1006\/jmbi.1994.0120","journal-title":"J Mol Biol"},{"issue":"5","key":"4015_CR23","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1006\/jmbi.1994.0190","volume":"247","author":"AV Sivolob","year":"1995","unstructured":"Sivolob AV, Khrapunov SN: Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness. J Mol Biol 1995, 247(5):918\u2013931. 10.1006\/jmbi.1994.0190","journal-title":"J Mol Biol"},{"issue":"1","key":"4015_CR24","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1006\/jmbi.1999.3236","volume":"295","author":"MJ Packer","year":"2000","unstructured":"Packer MJ, Dauncey MP, Hunter CA: Sequence-dependent DNA structure: dinucleotide conformational maps. J Mol Biol 2000, 295(1):71\u201383. 10.1006\/jmbi.1999.3236","journal-title":"J Mol Biol"},{"issue":"14","key":"4015_CR25","doi-asserted-by":"publisher","first-page":"3323","DOI":"10.1093\/nar\/26.14.3323","volume":"26","author":"RD Blake","year":"1998","unstructured":"Blake RD, Delcourt SG: Thermal stability of DNA. Nucleic Acids Res 1998, 26(14):3323\u20133332. 10.1093\/nar\/26.14.3323","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"4015_CR26","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1093\/bioinformatics\/15.5.370","volume":"15","author":"RD Blake","year":"1999","unstructured":"Blake RD, Bizzaro JW, Blake JD, Day GR, Delcourt SG, Knowles J, Marx KA, SantaLucia J Jr: Statistical mechanical simulation of polymeric DNA melting with MELTSIM. Bioinformatics 1999, 15(5):370\u2013375. 10.1093\/bioinformatics\/15.5.370","journal-title":"Bioinformatics"},{"issue":"11","key":"4015_CR27","doi-asserted-by":"publisher","first-page":"3746","DOI":"10.1073\/pnas.83.11.3746","volume":"83","author":"KJ Breslauer","year":"1986","unstructured":"Breslauer KJ, Frank R, Blocker H, Marky LA: Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83(11):3746\u20133750. 10.1073\/pnas.83.11.3746","journal-title":"Proc Natl Acad Sci USA"},{"issue":"22","key":"4015_CR28","doi-asserted-by":"publisher","first-page":"4501","DOI":"10.1093\/nar\/24.22.4501","volume":"24","author":"N Sugimoto","year":"1996","unstructured":"Sugimoto N, Nakano S, Yoneyama M, Honda K: Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 1996, 24(22):4501\u20134505. 10.1093\/nar\/24.22.4501","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"4015_CR29","doi-asserted-by":"publisher","first-page":"R263","DOI":"10.1186\/gb-2007-8-12-r263","volume":"8","author":"JR Goni","year":"2007","unstructured":"Goni JR, Perez A, Torrents D, Orozco M: Determining promoter location based on DNA structure first-principles calculations. Genome Biol 2007, 8(12):R263. 10.1186\/gb-2007-8-12-r263","journal-title":"Genome Biol"},{"issue":"1","key":"4015_CR30","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1006\/jmbi.1996.0304","volume":"259","author":"MA el Hassan","year":"1996","unstructured":"el Hassan MA, Calladine CR: Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol 1996, 259(1):95\u2013103. 10.1006\/jmbi.1996.0304","journal-title":"J Mol Biol"},{"issue":"19","key":"4015_CR31","doi-asserted-by":"publisher","first-page":"11163","DOI":"10.1073\/pnas.95.19.11163","volume":"95","author":"WK Olson","year":"1998","unstructured":"Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB: DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998, 95(19):11163\u201311168. 10.1073\/pnas.95.19.11163","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1-2","key":"4015_CR32","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1002\/bip.360300115","volume":"30","author":"PS Ho","year":"1990","unstructured":"Ho PS, Zhou GW, Clark LB: Polarized electronic spectra of Z-DNA single crystals. Biopolymers 1990, 30(1\u20132):151\u2013163. 10.1002\/bip.360300115","journal-title":"Biopolymers"},{"issue":"8","key":"4015_CR33","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1002\/j.1460-2075.1995.tb07169.x","volume":"14","author":"I Brukner","year":"1995","unstructured":"Brukner I, Sanchez R, Suck D, Pongor S: Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J 1995, 14(8):1812\u20131818.","journal-title":"EMBO J"},{"issue":"4","key":"4015_CR34","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/0022-2836(86)90452-3","volume":"191","author":"SC Satchwell","year":"1986","unstructured":"Satchwell SC, Drew HR, Travers AA: Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 1986, 191(4):659\u2013675. 10.1016\/0022-2836(86)90452-3","journal-title":"J Mol Biol"},{"issue":"1","key":"4015_CR35","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1006\/jmbi.1999.3237","volume":"295","author":"MJ Packer","year":"2000","unstructured":"Packer MJ, Dauncey MP, Hunter CA: Sequence-dependent DNA structure: tetranucleotide conformational maps. J Mol Biol 2000, 295(1):85\u2013103. 10.1006\/jmbi.1999.3237","journal-title":"J Mol Biol"},{"issue":"12","key":"4015_CR36","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1109\/10.335859","volume":"41","author":"I Cosic","year":"1994","unstructured":"Cosic I: Macromolecular bioactivity: is it resonant interaction between macromolecules?--Theory and applications. IEEE Trans Biomed Eng 1994, 41(12):1101\u20131114. 10.1109\/10.335859","journal-title":"IEEE Trans Biomed Eng"},{"key":"4015_CR37","unstructured":"FANTOM4 Project[http:\/\/fantom.gsc.riken.jp\/4\/]"},{"issue":"1","key":"4015_CR38","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.immuni.2008.12.009","volume":"30","author":"G Wei","year":"2009","unstructured":"Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, et al.: Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity 2009, 30(1):155\u2013167. 10.1016\/j.immuni.2008.12.009","journal-title":"Immunity"},{"issue":"7153","key":"4015_CR39","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/nature06008","volume":"448","author":"TS Mikkelsen","year":"2007","unstructured":"Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448(7153):553\u2013560. 10.1038\/nature06008","journal-title":"Nature"},{"issue":"7200","key":"4015_CR40","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/nature07056","volume":"454","author":"TS Mikkelsen","year":"2008","unstructured":"Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A: Dissecting direct reprogramming through integrative genomic analysis. Nature 2008, 454(7200):49\u201355. 10.1038\/nature07056","journal-title":"Nature"},{"issue":"7205","key":"4015_CR41","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/nature07107","volume":"454","author":"A Meissner","year":"2008","unstructured":"Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al.: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454(7205):766\u2013770.","journal-title":"Nature"},{"issue":"21","key":"4015_CR42","doi-asserted-by":"publisher","first-page":"2953","DOI":"10.1101\/gad.501108","volume":"22","author":"R Nielsen","year":"2008","unstructured":"Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbaek R, Megens E, Denissov S, Borgesen M, Francoijs KJ, Mandrup S, et al.: Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev 2008, 22(21):2953\u20132967. 10.1101\/gad.501108","journal-title":"Genes Dev"},{"issue":"11","key":"4015_CR43","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1038\/nbt1032","volume":"22","author":"VB Bajic","year":"2004","unstructured":"Bajic VB, Tan SL, Suzuki Y, Sugano S: Promoter prediction analysis on the whole human genome. Nat Biotechnol 2004, 22(11):1467\u20131473. 10.1038\/nbt1032","journal-title":"Nat Biotechnol"},{"issue":"12","key":"4015_CR44","doi-asserted-by":"publisher","first-page":"i313","DOI":"10.1093\/bioinformatics\/btp191","volume":"25","author":"T Abeel","year":"2009","unstructured":"Abeel T, Peer Y, Saeys Y: Toward a gold standard for promoter prediction evaluation. Bioinformatics 2009, 25(12):i313\u2013320. 10.1093\/bioinformatics\/btp191","journal-title":"Bioinformatics"},{"issue":"3","key":"4015_CR45","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1101\/gr.216102","volume":"12","author":"TA Down","year":"2002","unstructured":"Down TA, Hubbard TJ: Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002, 12(3):458\u2013461. 10.1101\/gr.216102","journal-title":"Genome Res"},{"issue":"4","key":"4015_CR46","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1038\/ng780","volume":"29","author":"RV Davuluri","year":"2001","unstructured":"Davuluri RV, Grosse I, Zhang MQ: Computational identification of promoters and first exons in the human genome. Nat Genet 2001, 29(4):412\u2013417. 10.1038\/ng780","journal-title":"Nat Genet"},{"issue":"13","key":"4015_CR47","doi-asserted-by":"publisher","first-page":"i24","DOI":"10.1093\/bioinformatics\/btn172","volume":"24","author":"T Abeel","year":"2008","unstructured":"Abeel T, Saeys Y, Rouze P, Peer Y: ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 2008, 24(13):i24\u201331. 10.1093\/bioinformatics\/btn172","journal-title":"Bioinformatics"},{"key":"4015_CR48","doi-asserted-by":"crossref","unstructured":"Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154\u2013158.","DOI":"10.1093\/nar\/gkm952"},{"issue":"7235","key":"4015_CR49","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/nature07672","volume":"458","author":"M Guttman","year":"2009","unstructured":"Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al.: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458(7235):223\u2013227. 10.1038\/nature07672","journal-title":"Nature"},{"issue":"2","key":"4015_CR50","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1101\/gr.081638.108","volume":"19","author":"X Wang","year":"2009","unstructured":"Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ: High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res 2009, 19(2):266\u2013275. 10.1101\/gr.081638.108","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S1-S65.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T04:28:10Z","timestamp":1630470490000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-S1-S65"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1]]},"references-count":50,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2010,1]]}},"alternative-id":["4015"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-s1-s65","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1]]},"assertion":[{"value":"18 January 2010","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S65"}}