{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T04:19:52Z","timestamp":1754108392610},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data &amp; annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Description<\/jats:title>\n            <jats:p>The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns\/exons and 'terminating' polyA site are delineated; EST\/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.ebi.ac.uk\/atd\/\" ext-link-type=\"uri\">http:\/\/www.ebi.ac.uk\/atd\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-169","type":"journal-article","created":{"date-parts":[[2006,4,6]],"date-time":"2006-04-06T12:49:19Z","timestamp":1144327759000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation"],"prefix":"10.1186","volume":"7","author":[{"given":"Vincent","family":"Le Texier","sequence":"first","affiliation":[]},{"given":"Jean-Jack","family":"Riethoven","sequence":"additional","affiliation":[]},{"given":"Vasudev","family":"Kumanduri","sequence":"additional","affiliation":[]},{"given":"Chellappa","family":"Gopalakrishnan","sequence":"additional","affiliation":[]},{"given":"Fabrice","family":"Lopez","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Gautheret","sequence":"additional","affiliation":[]},{"given":"Thangavel Alphonse","family":"Thanaraj","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,3,23]]},"reference":[{"key":"908_CR1","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1016\/j.tig.2003.09.014","volume":"19","author":"JR Landry","year":"2003","unstructured":"Landry JR, Mager DL, Wilhelm BT: Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet 2003, 19: 640\u2013648. 10.1016\/j.tig.2003.09.014","journal-title":"Trends Genet"},{"key":"908_CR2","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/S0968-0004(00)01604-2","volume":"25","author":"CW Smith","year":"2000","unstructured":"Smith CW, Valcarcel J: Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci 2000, 25: 381\u2013388. 10.1016\/S0968-0004(00)01604-2","journal-title":"Trends Biochem Sci"},{"key":"908_CR3","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1093\/nar\/gki158","volume":"33","author":"B Tian","year":"2005","unstructured":"Tian B, Hu J, Zhang H, Lutz CS: A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005, 33: 201\u2013212. 10.1093\/nar\/gki158","journal-title":"Nucleic Acids Res"},{"key":"908_CR4","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1101\/gr.1017303","volume":"13","author":"M Zavolan","year":"2003","unstructured":"Zavolan M, Kondo S, Sch\u00f6nbach C, Adachi J, Hume DA, RIKEN GER Group, Members GSL, Hayashizaki Y, Gaasterland T: Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome. Genome Res 2003, 13: 1290\u20131300. 10.1101\/gr.1017303","journal-title":"Genome Res"},{"key":"908_CR5","doi-asserted-by":"publisher","first-page":"11456","DOI":"10.1073\/pnas.94.21.11456","volume":"94","author":"P Cramer","year":"1997","unstructured":"Cramer P, Pesce CG, Baralle FE, Kornblihtt AR: Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci USA 1997, 94: 11456\u201311460. 10.1073\/pnas.94.21.11456","journal-title":"Proc Natl Acad Sci USA"},{"key":"908_CR6","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1093\/nar\/gkh076","volume":"32","author":"Y Suzuki","year":"2004","unstructured":"Suzuki Y, Yamashita R, Sugano S, Nakai K: DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res 2004, 32: 78\u201381. 10.1093\/nar\/gkh076","journal-title":"Nucleic Acids Res"},{"key":"908_CR7","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1101\/gr.794803","volume":"13","author":"ND Trinklein","year":"2003","unstructured":"Trinklein ND, Aldred SJF, Saldanha AJ, Myers RM: Identification and Functional Analysis of Human Transcriptional Promoters. Genome Res 2003, 13: 308\u2013312. 10.1101\/gr.794803","journal-title":"Genome Res"},{"key":"908_CR8","doi-asserted-by":"publisher","first-page":"3554","DOI":"10.1093\/nar\/gkg549","volume":"31","author":"AS Halees","year":"2003","unstructured":"Halees AS, Leyfer D, Weng Z: PromoSer: a large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res 2003, 31: 3554\u20133559. 10.1093\/nar\/gkg549","journal-title":"Nucleic Acids Res"},{"key":"908_CR9","doi-asserted-by":"publisher","first-page":"D82","DOI":"10.1093\/nar\/gkh122","volume":"32","author":"CD Schmid","year":"2004","unstructured":"Schmid CD, Praz V, Delorenzi M, P\u00e9rier R, Bucher P: The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res 2004, 32: D82\u201385. 10.1093\/nar\/gkh122","journal-title":"Nucleic Acids Res"},{"key":"908_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-662-09728-1_1","volume":"31","author":"TA Thanaraj","year":"2003","unstructured":"Thanaraj TA, Stamm S: Prediction and statistical analysis of alternatively spliced exons. Progress in Molecular and Subcellular Biology 2003, 31: 1\u201331.","journal-title":"Progress in Molecular and Subcellular Biology"},{"key":"908_CR11","doi-asserted-by":"publisher","first-page":"D64","DOI":"10.1093\/nar\/gkh030","volume":"32","author":"TA Thanaraj","year":"2004","unstructured":"Thanaraj TA, Stamm S, Clark F, Riethoven J-JM, Le Texier V, Muilu J: ASD: the Alternative Splicing Database. Nucleic Acids Res 2004, 32: D64-D69. 10.1093\/nar\/gkh030","journal-title":"Nucleic Acids Res"},{"key":"908_CR12","doi-asserted-by":"publisher","first-page":"D46","DOI":"10.1093\/nar\/gkj031","volume":"34","author":"S Stamm","year":"2006","unstructured":"Stamm S, Riethoven J-JM, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA: ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 2006, 34: D46-D55. 10.1093\/nar\/gkj031","journal-title":"Nucleic Acids Res"},{"key":"908_CR13","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1093\/hmg\/11.4.451","volume":"11","author":"F Clark","year":"2002","unstructured":"Clark F, Thanaraj TA: Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Hum Mol Genet 2002, 11: 451\u2013464. 10.1093\/hmg\/11.4.451","journal-title":"Hum Mol Genet"},{"key":"908_CR14","doi-asserted-by":"publisher","first-page":"3977","DOI":"10.1093\/nar\/gkh731","volume":"32","author":"J Leipzig","year":"2004","unstructured":"Leipzig J, Pevzner P, Heber S: The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res 2004, 32: 3977\u20133983. 10.1093\/nar\/gkh731","journal-title":"Nucleic Acids Res"},{"key":"908_CR15","first-page":"78","volume":"9","author":"CL Zheng","year":"2004","unstructured":"Zheng CL, Nair TM, Gribskov M, Kwon YS, Li HR, Fu XD: Manually Annotated Alternatively Spliced Events (MAASE) database. Pac Symp Biocomput 2004, 9: 78\u201388.","journal-title":"Pac Symp Biocomput"},{"key":"908_CR16","doi-asserted-by":"publisher","first-page":"R29","DOI":"10.1186\/gb-2003-4-4-r29","volume":"4","author":"HD Huang","year":"2003","unstructured":"Huang HD, Horng JT, Lee CC, Liu BJ: ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. Genome Biol 2003, 4: R29. 10.1186\/gb-2003-4-4-r29","journal-title":"Genome Biol"},{"key":"908_CR17","doi-asserted-by":"publisher","first-page":"D75","DOI":"10.1093\/nar\/gki118","volume":"33","author":"P Kim","year":"2005","unstructured":"Kim P, Kim N, Lee Y, Kim B, Shin Y, Lee S: ECgene: genome annotation for alternative splicing. Nucleic Acids Res 2005, 33: D75-D79. 10.1093\/nar\/gki118","journal-title":"Nucleic Acids Res"},{"key":"908_CR18","doi-asserted-by":"publisher","first-page":"D80","DOI":"10.1093\/nar\/gki129","volume":"33","author":"H-D Huang","year":"2005","unstructured":"Huang H-D, Horng J-T, Lin F-M, Chang Y-C, Huang C-C: SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res 2005, 33: D80-D85. 10.1093\/nar\/gki129","journal-title":"Nucleic Acids Res"},{"key":"908_CR19","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1093\/nar\/gkh136","volume":"32","author":"H Pospisil","year":"2004","unstructured":"Pospisil H, Herrmann A, Bortfeldt RH, Reich JG: EASED:Extended Alternatively Spliced EST Database. Nucleic Acids Res 2004, 32: 70\u201374. 10.1093\/nar\/gkh136","journal-title":"Nucleic Acids Res"},{"key":"908_CR20","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1093\/nar\/29.1.260","volume":"29","author":"H Ji","year":"2001","unstructured":"Ji H, Zhou Q, Wen F, Xia H, Lu X, Li Y: AsMamDB: an alternative splice database of mammals. Nucleic Acids Res 2001, 29: 260\u2013263. 10.1093\/nar\/29.1.260","journal-title":"Nucleic Acids Res"},{"key":"908_CR21","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1093\/nar\/28.1.296","volume":"28","author":"M Dralyuk","year":"2000","unstructured":"Dralyuk M, Brudno M, Gelfand MS, Zorn M, Dubchak I: ASDB: database of alternatively spliced genes. Nucleic Acids Res 2000, 28: 296\u2013297. 10.1093\/nar\/28.1.296","journal-title":"Nucleic Acids Res"},{"key":"908_CR22","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1093\/nar\/30.1.186","volume":"30","author":"Y-H Huang","year":"2002","unstructured":"Huang Y-H, Chen Y-T, Lai J-J, Yang S-T, Yang U-C: PALS db: Putative Alternative Splicing database. Nucleic Acids Res 2002, 30: 186\u2013190. 10.1093\/nar\/30.1.186","journal-title":"Nucleic Acids Res"},{"key":"908_CR23","doi-asserted-by":"publisher","first-page":"2579","DOI":"10.1093\/bioinformatics\/bth288","volume":"20","author":"S Gupta","year":"2004","unstructured":"Gupta S, Zink D, Korn B, Vingron M, Haas SA: Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 2004, 20: 2579\u20132585. 10.1093\/bioinformatics\/bth288","journal-title":"Bioinformatics"},{"key":"908_CR24","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/nar\/gkg029","volume":"31","author":"C Lee","year":"2003","unstructured":"Lee C, Atanelov L, Modrek B, Xing Y: ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 2003, 31: 101\u2013105. 10.1093\/nar\/gkg029","journal-title":"Nucleic Acids Res"},{"key":"908_CR25","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1101\/gr.190501","volume":"9","author":"E Beaudoing","year":"2001","unstructured":"Beaudoing E, Gautheret D: Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res 2001, 9: 1520\u20131526. 10.1101\/gr.190501","journal-title":"Genome Res"},{"key":"908_CR26","doi-asserted-by":"publisher","first-page":"D116","DOI":"10.1093\/nar\/gki055","volume":"33","author":"H Zhang","year":"2005","unstructured":"Zhang H, Hu J, Recce M, Tian B: PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res 2005, 33: D116-D120. 10.1093\/nar\/gki055","journal-title":"Nucleic Acids Res"},{"key":"908_CR27","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1101\/gr.155001","volume":"11","author":"Z Kan","year":"2001","unstructured":"Kan Z, Rouchka EC, Gish WR, States DJ: Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 2001, 11: 889\u2013900. 10.1101\/gr.155001","journal-title":"Genome Res"},{"key":"908_CR28","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1101\/gr.3109605","volume":"15","author":"J Yan","year":"2005","unstructured":"Yan J, Marr TG: Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res 2005, 15: 369\u201375. 10.1101\/gr.3109605","journal-title":"Genome Res"},{"key":"908_CR29","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/416499a","volume":"416","author":"T Maniatis","year":"2002","unstructured":"Maniatis T, Reed R: An extensive network of coupling among gene expression machines. Nature 2002, 416: 499\u2013506. 10.1038\/416499a","journal-title":"Nature"},{"key":"908_CR30","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1101\/gad.1093603","volume":"17","author":"O Calvo","year":"2003","unstructured":"Calvo O, Manley JL: Strange bedfellows: polyadenylation factors at the promoter. Genes Dev 2003, 17: 1321\u20131327. 10.1101\/gad.1093603","journal-title":"Genes Dev"},{"key":"908_CR31","doi-asserted-by":"publisher","first-page":"3865","DOI":"10.1242\/jcs.00073","volume":"115","author":"KM Neugebauer","year":"2002","unstructured":"Neugebauer KM: On the importance of being co-transcriptional. J. Cell. Sci 2002, 115: 3865\u20133871. 10.1242\/jcs.00073","journal-title":"J. Cell. Sci"},{"key":"908_CR32","doi-asserted-by":"publisher","first-page":"6261","DOI":"10.1242\/jcs.01513","volume":"117","author":"JR Sanford","year":"2004","unstructured":"Sanford JR, Caceres JF: Pre-mRNA splicing: life at the centre of the central dogma. J Cell Sci 2004, 117: 6261\u20136263. 10.1242\/jcs.01513","journal-title":"J Cell Sci"},{"key":"908_CR33","doi-asserted-by":"publisher","first-page":"1489","DOI":"10.1261\/rna.7100104","volume":"10","author":"AR Kornblihtt","year":"2004","unstructured":"Kornblihtt AR, De La Mata M, Fededa JP, Munoz MJ, Nogues G: Multiple links between transcription and splicing. RNA 2004, 10: 1489\u20131498. 10.1261\/rna.7100104","journal-title":"RNA"},{"key":"908_CR34","doi-asserted-by":"publisher","first-page":"748","DOI":"10.1101\/gr.3269805","volume":"15","author":"A Sharov","year":"2005","unstructured":"Sharov A, Dudekula DB, Ko MSH: Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res 2005, 15: 748\u2013754. 10.1101\/gr.3269805","journal-title":"Genome Res"},{"key":"908_CR35","doi-asserted-by":"publisher","first-page":"D447","DOI":"10.1093\/nar\/gki138","volume":"33","author":"T Hubbard","year":"2005","unstructured":"Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E: Ensembl 2005. Nucleic Acids Res 2005, 33: D447-D453. 10.1093\/nar\/gki138","journal-title":"Nucleic Acids Res"},{"key":"908_CR36","doi-asserted-by":"publisher","first-page":"D29","DOI":"10.1093\/nar\/gki098","volume":"33","author":"C Kanz","year":"2005","unstructured":"Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, Bates K, Browne P, van den Broek A, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Gamble J, Diez FG, Harte N, Kulikova T, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Sobhany S, Stoehr P, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R: The EMBL Nucleotide Sequence Database. Nucleic Acids Res 2005, 33: D29-D33. 10.1093\/nar\/gki098","journal-title":"Nucleic Acids Res"},{"key":"908_CR37","doi-asserted-by":"publisher","first-page":"1690","DOI":"10.1093\/nar\/29.8.1690","volume":"29","author":"E Pauws","year":"2001","unstructured":"Pauws E, van Kampen AH, van de Graaf SA, de Vijlder JJ, Ris-Stalpers C: Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res 2001, 29: 1690\u20131694. 10.1093\/nar\/29.8.1690","journal-title":"Nucleic Acids Res"},{"key":"908_CR38","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/ng0893-332","volume":"4","author":"MS Boguski","year":"1993","unstructured":"Boguski MS, Lowe TM, Tolstoshev CM: dbEST--database for expressed sequence tags. Nat Genet 1993, 4: 332\u2013333. 10.1038\/ng0893-332","journal-title":"Nat Genet"},{"key":"908_CR39","doi-asserted-by":"publisher","first-page":"856","DOI":"10.1371\/journal.pbio.0020162","volume":"2","author":"T Imanishi","year":"2004","unstructured":"Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Ya-masaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Mde FBM, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology 2004, 2: 856\u2013875. 10.1371\/journal.pbio.0020162","journal-title":"PLoS Biology"},{"key":"908_CR40","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1101\/gr.1119703","volume":"13","author":"P Carninci","year":"2003","unstructured":"Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y: Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia. Genome Res 2003, 13: 1273\u20131289. 10.1101\/gr.1119703","journal-title":"Genome Res"},{"key":"908_CR41","doi-asserted-by":"publisher","first-page":"W20","DOI":"10.1093\/nar\/gkh435","volume":"32","author":"S Mcginnis","year":"2004","unstructured":"Mcginnis S, Madden T: BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004, 32: W20-W25. 10.1093\/nar\/gnh003","journal-title":"Nucleic Acids Res"},{"key":"908_CR42","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1126\/science.1090100","volume":"302","author":"JM Johnson","year":"2003","unstructured":"Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction. Microarrays. Science 2003, 302: 2141\u20132144. 10.1126\/science.1090100","journal-title":"Science"},{"key":"908_CR43","doi-asserted-by":"publisher","first-page":"3392","DOI":"10.1093\/nar\/gkh656","volume":"32","author":"A Hajarnavis","year":"2004","unstructured":"Hajarnavis A, Korf I, Durbin R: A probabilistic model of 3' end formation in Caenorhabditis elegans . Nucleic Acids Res 2004, 32: 3392\u20133399. 10.1093\/nar\/gkh656","journal-title":"Nucleic Acids Res"},{"key":"908_CR44","doi-asserted-by":"publisher","first-page":"2544","DOI":"10.1093\/nar\/gkg355","volume":"31","author":"TA Thanaraj","year":"2003","unstructured":"Thanaraj TA, Clark F, Muilu J: Conservation of human alternative splice events in mouse. Nucleic Acids Res 2003, 31: 2544\u20132552. 10.1093\/nar\/gkg355","journal-title":"Nucleic Acids Res"},{"key":"908_CR45","doi-asserted-by":"publisher","first-page":"D154","DOI":"10.1093\/nar\/gki070","volume":"33","author":"A Bairoch","year":"2005","unstructured":"Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005, 33: D154\u2013159. 10.1093\/nar\/gki070","journal-title":"Nucleic Acids Res"},{"key":"908_CR46","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1093\/nar\/30.1.169","volume":"30","author":"HM Wain","year":"2002","unstructured":"Wain HM, Lush M, Ducluzeau F, Povey S: Genew: the Human Gene Nomenclature Database. Nucleic Acids Res 2002, 30: 169\u2013171. 10.1093\/nar\/30.1.169","journal-title":"Nucleic Acids Res"},{"key":"908_CR47","doi-asserted-by":"publisher","first-page":"1425","DOI":"10.1101\/gr.180801","volume":"11","author":"M Ashburner","year":"2001","unstructured":"Ashburner M, Ball CA, Blake JA, Butler H, Cherry JM, Corradi J, Dolinski K, Janan T, Eppig JT, Harris M, Hill DP, Lewis S, Marshall B, Mungall C, Reiser L, Rhee S, Richardson JE, Richter J, Ringwald M, Rubin GM, Sherlock G, Yoon J: Creating the Gene Ontology resource: design and implementation. Genome Res 2001, 11: 1425\u20131433. 10.1101\/gr.180801","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-169.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:04:05Z","timestamp":1630494245000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-169"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,3,23]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["908"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-169","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,3,23]]},"assertion":[{"value":"14 December 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 March 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 March 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"169"}}