{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T08:27:07Z","timestamp":1768292827487,"version":"3.49.0"},"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2009,9,2]],"date-time":"2009-09-02T00:00:00Z","timestamp":1251849600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0006849","type":"journal-article","created":{"date-parts":[[2009,9,1]],"date-time":"2009-09-01T22:03:20Z","timestamp":1251842600000},"page":"e6849","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":41,"title":["Genome-Wide Analysis of Small RNA and Novel MicroRNA Discovery in Human Acute Lymphoblastic Leukemia Based on Extensive Sequencing Approach"],"prefix":"10.1371","volume":"4","author":[{"given":"Hua","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian-Hua","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Sheng","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xue-Qun","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi-Yong","family":"Ke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang-Hu","family":"Qu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue-Qin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2009,9,2]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function.","volume":"116","author":"DP Bartel","year":"2004","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1093\/nar\/gki200","article-title":"Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis.","volume":"33","author":"AM Cheng","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"7390","DOI":"10.1158\/0008-5472.CAN-06-0800","article-title":"MicroRNA-cancer connection: the beginning of a new tale.","volume":"66","author":"GA Calin","year":"2006","journal-title":"Cancer Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1073\/pnas.0307323101","article-title":"Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers.","volume":"101","author":"GA Calin","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ydbio.2006.08.028","article-title":"microRNAs as oncogenes and tumor suppressors.","volume":"302","author":"B Zhang","year":"2007","journal-title":"Dev Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.1056\/NEJMp058190","article-title":"MicroRNAs as oncogenes and tumor suppressors.","volume":"353","author":"CZ Chen","year":"2005","journal-title":"N Engl J Med"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nrc1840","article-title":"Oncomirs - microRNAs with a role in cancer.","volume":"6","author":"A Esquela-Kerscher","year":"2006","journal-title":"Nat Rev Cancer"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1101\/gad.1705308","article-title":"Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.","volume":"22","author":"JE Babiarz","year":"2008","journal-title":"Genes Dev"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1101\/gr.5159906","article-title":"Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis.","volume":"16","author":"E Berezikov","year":"2006","journal-title":"Genome Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1101\/gr.074740.107","article-title":"A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.","volume":"18","author":"EA Glazov","year":"2008","journal-title":"Genome Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1016\/j.cell.2007.04.040","article-title":"A mammalian microRNA expression atlas based on small RNA library sequencing.","volume":"129","author":"P Landgraf","year":"2007","journal-title":"Cell"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"6031","DOI":"10.1158\/0008-5472.CAN-06-0561","article-title":"Patterns of known and novel small RNAs in human cervical cancer.","volume":"67","author":"WO Lui","year":"2007","journal-title":"Cancer Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1016\/j.cell.2006.10.040","article-title":"Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.","volume":"127","author":"JG Ruby","year":"2006","journal-title":"Cell"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1101\/gr.7179508","article-title":"Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.","volume":"18","author":"RD Morin","year":"2008","journal-title":"Genome Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/sj.leu.2405022","article-title":"Small RNAs analysis in CLL reveals a deregulation of miRNA expression and novel miRNA candidates of putative relevance in CLL pathogenesis.","volume":"22","author":"S Marton","year":"2008","journal-title":"Leukemia"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1038\/sj.leu.2405031","article-title":"MicroRNA expression profiles of human leukemias.","volume":"22","author":"S Takada","year":"2008","journal-title":"Leukemia"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1101\/gr.077578.108","article-title":"In-depth characterization of the microRNA transcriptome in a leukemia progression model.","volume":"18","author":"F Kuchenbauer","year":"2008","journal-title":"Genome Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1016\/S0140-6736(08)60457-2","article-title":"Acute lymphoblastic leukaemia.","volume":"371","author":"CH Pui","year":"2008","journal-title":"Lancet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1002\/cncr.11664","article-title":"The biology and therapy of adult acute lymphoblastic leukemia.","volume":"98","author":"S Faderl","year":"2003","journal-title":"Cancer"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1182\/blood.V99.3.825","article-title":"Double-delayed intensification improves event-free survival for children with intermediate-risk acute lymphoblastic leukemia: a report from the Children's Cancer Group.","volume":"99","author":"BJ Lange","year":"2002","journal-title":"Blood"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1200\/JCO.2003.03.009","article-title":"Intensification of therapy for children with lower-risk acute lymphoblastic leukemia: long-term follow-up of patients treated on Children's Cancer Group Trial 1881.","volume":"21","author":"RJ Hutchinson","year":"2003","journal-title":"J Clin Oncol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"3809","DOI":"10.1182\/blood-2002-08-2454","article-title":"Dexamethasone versus prednisone and daily oral versus weekly intravenous mercaptopurine for patients with standard-risk acute lymphoblastic leukemia: a report from the Children's Cancer Group.","volume":"101","author":"BC Bostrom","year":"2003","journal-title":"Blood"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/S1470-2045(08)70070-6","article-title":"Current management and challenges of malignant disease in the CNS in paediatric leukaemia.","volume":"9","author":"CH Pui","year":"2008","journal-title":"Lancet Oncol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/leu.2008.286","article-title":"Identification of new microRNA genes and aberrant microRNA profiles in childhood acute lymphoblastic leukemia.","volume":"23","author":"D Schotte","year":"2009","journal-title":"Leukemia"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03702","article-title":"MicroRNA expression profiles classify human cancers.","volume":"435","author":"J Lu","year":"2005","journal-title":"Nature"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"19971","DOI":"10.1073\/pnas.0709313104","article-title":"MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia.","volume":"104","author":"S Mi","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1590\/S0100-879X2007001100003","article-title":"miRNA expression profiles in chronic lymphocytic and acute lymphocytic leukemia.","volume":"40","author":"DL Zanette","year":"2007","journal-title":"Braz J Med Biol Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1101\/gad.1074403","article-title":"The microRNAs of Caenorhabditis elegans.","volume":"17","author":"LP Lim","year":"2003","journal-title":"Genes Dev"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1038\/nsmb.1409","article-title":"The regulatory activity of microRNA* species has substantial influence on microRNA and 3\u2032 UTR evolution.","volume":"15","author":"K Okamura","year":"2008","journal-title":"Nat Struct Mol Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1093\/bioinformatics\/bth374","article-title":"Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.","volume":"20","author":"E Bonnet","year":"2004","journal-title":"Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1261\/rna.7220505","article-title":"Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.","volume":"11","author":"P Clote","year":"2005","journal-title":"Rna"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1073\/pnas.0409169102","article-title":"Fast and reliable prediction of noncoding RNAs.","volume":"102","author":"S Washietl","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nbt1394","article-title":"Discovering microRNAs from deep sequencing data using miRDeep.","volume":"26","author":"MR Friedlander","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/S0092-8674(03)01018-3","article-title":"Prediction of mammalian microRNA targets.","volume":"115","author":"BP Lewis","year":"2003","journal-title":"Cell"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","article-title":"Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.","volume":"120","author":"BP Lewis","year":"2005","journal-title":"Cell"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"3338","DOI":"10.1093\/nar\/gkl428","article-title":"Comprehensive thermodynamic analysis of 3\u2032 double-nucleotide overhangs neighboring Watson-Crick terminal base pairs.","volume":"34","author":"AS O'Toole","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"5944","DOI":"10.1093\/nar\/gkm641","article-title":"Tissue-dependent paired expression of miRNAs.","volume":"35","author":"S Ro","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.cub.2007.12.049","article-title":"Argonaute loading improves the 5\u2032 precision of both MicroRNAs and their miRNA strands in flies.","volume":"18","author":"H Seitz","year":"2008","journal-title":"Curr Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1080\/10245330600938125","article-title":"Expression of apoptosis regulators Bcl-2 and Bax in childhood acute lymphoblastic leukemia.","volume":"12","author":"S Narayan","year":"2007","journal-title":"Hematology"},{"key":"ref41","first-page":"318","article-title":"Abnormalities of the P53, MDM2, BCL2 and BAX genes in acute leukemias.","volume":"52","author":"I Wojcik","year":"2005","journal-title":"Neoplasma"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"2300","DOI":"10.1182\/blood-2007-06-098012","article-title":"BCL-2 dependence and ABT-737 sensitivity in acute lymphoblastic leukemia.","volume":"111","author":"V Del Gaizo Moore","year":"2008","journal-title":"Blood"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1111\/j.1365-2141.2008.07329.x","article-title":"The subcellular Sox11 distribution pattern identifies subsets of mantle cell lymphoma: correlation to overall survival.","volume":"143","author":"X Wang","year":"2008","journal-title":"Br J Haematol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"3475","DOI":"10.1101\/gad.403406","article-title":"The establishment of neuronal properties is controlled by Sox4 and Sox11.","volume":"20","author":"M Bergsland","year":"2006","journal-title":"Genes Dev"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1200\/JCO.2003.10.032","article-title":"Toward optimal central nervous system-directed treatment in childhood acute lymphoblastic leukemia.","volume":"21","author":"CH Pui","year":"2003","journal-title":"J Clin Oncol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1101\/gr.7.10.986","article-title":"The significance of digital gene expression profiles.","volume":"7","author":"S Audic","year":"1997","journal-title":"Genome Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures.","volume":"125","author":"FW Hofacker IL","year":"1994","journal-title":"Monatsh Chem"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/bioinformatics\/btk010","article-title":"RNAshapes: an integrated RNA analysis package based on abstract shapes.","volume":"22","author":"P Steffen","year":"2006","journal-title":"Bioinformatics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1093\/bioinformatics\/btg114","article-title":"GeneMerge\u2014post-genomic analysis, data mining, and hypothesis testing.","volume":"19","author":"CI Castillo-Davis","year":"2003","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/j.cub.2006.01.050","article-title":"A genome-wide map of conserved microRNA targets in C. elegans.","volume":"16","author":"S Lall","year":"2006","journal-title":"Curr Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","article-title":"TM4: a free, open-source system for microarray data management and analysis.","volume":"34","author":"AI Saeed","year":"2003","journal-title":"Biotechniques"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"e179","DOI":"10.1093\/nar\/gni178","article-title":"Real-time quantification of microRNAs by stem-loop RT-PCR.","volume":"33","author":"C Chen","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.","volume":"25","author":"KJ Livak","year":"2001","journal-title":"Methods"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0006849","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T09:29:50Z","timestamp":1558517390000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0006849"}},"subtitle":[],"editor":[{"given":"Baohong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2009,9,2]]},"references-count":54,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2009,9,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0006849","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,9,2]]}}}