{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T04:10:19Z","timestamp":1750306219486,"version":"3.41.0"},"reference-count":88,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,5,4]],"date-time":"2017-05-04T00:00:00Z","timestamp":1493856000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U01CA166886","1U01AR069395","1R01GM123037","1U01HL111560"],"award-info":[{"award-number":["1U01CA166886","1U01AR069395","1R01GM123037","1U01HL111560"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["61373105","61672422"],"award-info":[{"award-number":["61373105","61672422"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01LM010185","1U01CA166886"],"award-info":[{"award-number":["1R01LM010185","1U01CA166886"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Long non-coding RNAs (lncRNAs) have been implicated in the regulation of diverse biological functions. The number of newly identified lncRNAs has increased dramatically in recent years but their expression and function have not yet been described from most diseases. To elucidate lncRNA function in human disease, we have developed a novel network based method (NLCFA) integrating correlations between lncRNA, protein coding genes and noncoding miRNAs. We have also integrated target gene associations and protein-protein interactions and designed our model to provide information on the combined influence of mRNAs, lncRNAs and miRNAs on cellular signal transduction networks.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We have generated lncRNA expression profiles from the CD34+\u2009haematopoietic stem and progenitor cells (HSPCs) from patients with Myelodysplastic syndromes (MDS) and healthy donors. We report, for the first time, aberrantly expressed lncRNAs in MDS and further prioritize biologically relevant lncRNAs using the NLCFA. Taken together, our data suggests that aberrant levels of specific lncRNAs are intimately involved in network modules that control multiple cancer-associated signalling pathways and cellular processes. Importantly, our method can be applied to prioritize aberrantly expressed lncRNAs for functional validation in other diseases and biological contexts.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The method is implemented in R language and Matlab.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx280","type":"journal-article","created":{"date-parts":[[2017,5,3]],"date-time":"2017-05-03T19:11:11Z","timestamp":1493838671000},"page":"2622-2630","source":"Crossref","is-referenced-by-count":12,"title":["Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method"],"prefix":"10.1093","volume":"33","author":[{"given":"Keqin","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA"}]},{"given":"Dominik","family":"Beck","sequence":"additional","affiliation":[{"name":"Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, Australia"},{"name":"Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, Australia"}]},{"given":"Julie A I","family":"Thoms","sequence":"additional","affiliation":[{"name":"Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, Australia"}]},{"given":"Liang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA"}]},{"given":"Weiling","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA"}]},{"given":"John E","family":"Pimanda","sequence":"additional","affiliation":[{"name":"Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, Australia"},{"name":"Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, Australia"},{"name":"Department of Haematology, Prince of Wales Hospital, Randwick, NSW, Australia"}]},{"given":"Xiaobo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,5,4]]},"reference":[{"key":"2023020206283540600_btx280-B1","first-page":"1124","article-title":"Myelodysplastic syndromes: recent advances","volume":"86","author":"Alessandrino","year":"2001","journal-title":"Haematologica"},{"key":"2023020206283540600_btx280-B2","doi-asserted-by":"crossref","first-page":"13613","DOI":"10.1073\/pnas.0405454101","article-title":"Proteasomal degradation of the FoxO1 transcriptional regulator in cells transformed by the P3k and Akt oncoproteins","volume":"101","author":"Aoki","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020206283540600_btx280-B3","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":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023020206283540600_btx280-B4","doi-asserted-by":"crossref","first-page":"2737","DOI":"10.1002\/ijc.24638","article-title":"Epigenetic regulation of microRNA expression in colorectal cancer","volume":"125","author":"Bandres","year":"2009","journal-title":"Int. J. Cancer"},{"key":"2023020206283540600_btx280-B5","doi-asserted-by":"crossref","first-page":"5282","DOI":"10.1073\/pnas.0810909106","article-title":"Induction and regulatory function of miR-9 in human monocytes and neutrophils exposed to proinflammatory signals","volume":"106","author":"Bazzoni","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020206283540600_btx280-B6","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1056\/NEJMoa1013343","article-title":"Clinical effect of point mutations in myelodysplastic syndromes","volume":"364","author":"Bejar","year":"2011","journal-title":"N. Engl. J. Med"},{"key":"2023020206283540600_btx280-B7","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate \u2013 a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. B Met"},{"key":"2023020206283540600_btx280-B8","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1111\/j.1365-2141.2008.07245.x","article-title":"Molecular pathways in myelodysplastic syndromes and acute myeloid leukemia: relationships and distinctions \u2013 a review","volume":"142","author":"Bernasconi","year":"2008","journal-title":"Br. J. Haematol"},{"key":"2023020206283540600_btx280-B9","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1002\/gcc.20549","article-title":"Amplification of 11q13 in ovarian carcinoma","volume":"47","author":"Brown","year":"2008","journal-title":"Genes Chromosomes Cancer"},{"key":"2023020206283540600_btx280-B10","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1101\/gad.17446611","article-title":"Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses","volume":"25","author":"Cabili","year":"2011","journal-title":"Genes Dev"},{"key":"2023020206283540600_btx280-B11","doi-asserted-by":"crossref","first-page":"15524","DOI":"10.1073\/pnas.242606799","article-title":"Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia","volume":"99","author":"Calin","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020206283540600_btx280-B12","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1038\/bjc.2013.233","article-title":"Long noncoding RNAs and the genetics of cancer","volume":"108","author":"Cheetham","year":"2013","journal-title":"Br. J. Cancer"},{"key":"2023020206283540600_btx280-B13","doi-asserted-by":"crossref","first-page":"16840.","DOI":"10.1038\/srep16840","article-title":"KATZLDA: KATZ measure for the lncRNA-disease association prediction","volume":"5","author":"Chen","year":"2015","journal-title":"Sci. Rep"},{"key":"2023020206283540600_btx280-B14","doi-asserted-by":"crossref","first-page":"13186.","DOI":"10.1038\/srep13186","article-title":"Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA","volume":"5","author":"Chen","year":"2015","journal-title":"Sci. Rep"},{"key":"2023020206283540600_btx280-B15","doi-asserted-by":"crossref","first-page":"45948","DOI":"10.18632\/oncotarget.10008","article-title":"FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model","volume":"7","author":"Chen","year":"2016","journal-title":"Oncotarget"},{"key":"2023020206283540600_btx280-B16","doi-asserted-by":"crossref","first-page":"57919","DOI":"10.18632\/oncotarget.11141","article-title":"IRWRLDA: improved random walk with restart for lncRNA-disease association prediction","volume":"7","author":"Chen","year":"2016","journal-title":"Oncotarget"},{"key":"2023020206283540600_btx280-B17","doi-asserted-by":"crossref","first-page":"2973","DOI":"10.1161\/01.CIR.0000039103.58920.1F","article-title":"Erythropoietin is a novel vascular protectant through activation of Akt1 and mitochondrial modulation of cysteine proteases","volume":"106","author":"Chong","year":"2002","journal-title":"Circulation"},{"key":"2023020206283540600_btx280-B18","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1038\/sj.bjp.0707161","article-title":"Erythropoietin involves the phosphatidylinositol 3-kinase pathway, 14-3-3 protein and FOXO3a nuclear trafficking to preserve endothelial cell integrity","volume":"150","author":"Chong","year":"2007","journal-title":"Br. J. Pharmacol"},{"key":"2023020206283540600_btx280-B19","doi-asserted-by":"crossref","first-page":"e1000384","DOI":"10.1371\/journal.pbio.1000384","article-title":"A large fraction of extragenic RNA pol II transcription sites overlap enhancers","volume":"8","author":"De Santa","year":"2010","journal-title":"PLoS Biol"},{"key":"2023020206283540600_btx280-B20","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1101\/gr.132159.111","article-title":"The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression","volume":"22","author":"Derrien","year":"2012","journal-title":"Genome Res"},{"key":"2023020206283540600_btx280-B21","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/ejhg.2010.209","article-title":"Distinctive microRNA expression profiles in CD34+ bone marrow cells from patients with myelodysplastic syndrome","volume":"19","author":"Dostalova Merkerova","year":"2011","journal-title":"Eur. J. Hum. Genet. EJHG"},{"key":"2023020206283540600_btx280-B22","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B23","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1038\/leu.2013.357","article-title":"miR-9 is a tumor suppressor in pediatric AML with t(8;21)","volume":"28","author":"Emmrich","year":"2014","journal-title":"Leukemia"},{"key":"2023020206283540600_btx280-B24","doi-asserted-by":"crossref","first-page":"13987","DOI":"10.1074\/jbc.M901758200","article-title":"MDM2 acts downstream of p53 as an E3 ligase to promote FOXO ubiquitination and degradation","volume":"284","author":"Fu","year":"2009","journal-title":"J. Biol. Chem"},{"key":"2023020206283540600_btx280-B25","doi-asserted-by":"crossref","first-page":"18679","DOI":"10.1073\/pnas.1422050112","article-title":"Expression and prognostic impact of lncRNAs in acute myeloid leukemia","volume":"111","author":"Garzon","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"year":"2013","author":"Goff","key":"2023020206283540600_btx280-B26"},{"key":"2023020206283540600_btx280-B27","doi-asserted-by":"crossref","first-page":"e35","DOI":"10.1093\/nar\/gks967","article-title":"Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks","volume":"41","author":"Guo","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B28","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nature07672","article-title":"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals","volume":"458","author":"Guttman","year":"2009","journal-title":"Nature"},{"key":"2023020206283540600_btx280-B29","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nature10398","article-title":"lincRNAs act in the circuitry controlling pluripotency and differentiation","volume":"477","author":"Guttman","year":"2011","journal-title":"Nature"},{"key":"2023020206283540600_btx280-B30","first-page":"53","article-title":"The World Health Organization classification of neoplasms of the hematopoietic and lymphoid tissues: report of the Clinical Advisory Committee meeting \u2013 Airlie House, Virginia, November, 1997","volume":"1","author":"Harris","year":"2000","journal-title":"Hematol. J. Off. J. Eur. Haematol. Assoc. EHA"},{"key":"2023020206283540600_btx280-B31","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1158\/1078-0432.CCR-11-2450","article-title":"Genome-wide miRNA expression profiling identifies miR-9-3 and miR-193a as targets for DNA methylation in non-small cell lung cancers","volume":"18","author":"Heller","year":"2012","journal-title":"Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res"},{"key":"2023020206283540600_btx280-B32","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1093\/jjco\/hyg037","article-title":"Molecular mechanisms of myelodysplastic syndrome","volume":"33","author":"Hirai","year":"2003","journal-title":"Jpn. J. Clin. Oncol"},{"key":"2023020206283540600_btx280-B33","doi-asserted-by":"crossref","first-page":"3265","DOI":"10.1182\/blood-2003-06-2124","article-title":"The WHO classification of MDS does make a difference","volume":"103","author":"Howe","year":"2004","journal-title":"Blood"},{"key":"2023020206283540600_btx280-B34","doi-asserted-by":"crossref","first-page":"5936","DOI":"10.1158\/0008-5472.CAN-08-4914","article-title":"Xenoestrogen-induced epigenetic repression of microRNA-9-3 in breast epithelial cells","volume":"69","author":"Hsu","year":"2009","journal-title":"Cancer Res"},{"key":"2023020206283540600_btx280-B35","doi-asserted-by":"crossref","first-page":"D163","DOI":"10.1093\/nar\/gkq1107","article-title":"miRTarBase: a database curates experimentally validated microRNA-target interactions","volume":"39","author":"Hsu","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B36","doi-asserted-by":"crossref","first-page":"C114","DOI":"10.4103\/0973-1482.145816","article-title":"Identification of melanoma biomarkers based on network modules by integrating the human signaling network with microarrays","volume":"10","author":"Huang","year":"2014","journal-title":"J. Cancer Res. Therap"},{"key":"2023020206283540600_btx280-B37","doi-asserted-by":"crossref","first-page":"25902","DOI":"10.18632\/oncotarget.8296","article-title":"ILNCSIM: improved lncRNA functional similarity calculation model","volume":"7","author":"Huang","year":"2016","journal-title":"Oncotarget"},{"key":"2023020206283540600_btx280-B38","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/j.cell.2010.06.040","article-title":"A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response","volume":"142","author":"Huarte","year":"2010","journal-title":"Cell"},{"key":"2023020206283540600_btx280-B39","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/ng.848","article-title":"Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters","volume":"43","author":"Hung","year":"2011","journal-title":"Nat. Genet"},{"key":"2023020206283540600_btx280-B40","doi-asserted-by":"crossref","first-page":"e363","DOI":"10.1371\/journal.pbio.0020363","article-title":"Human MicroRNA targets","volume":"2","author":"John","year":"2004","journal-title":"PLoS Biol"},{"key":"2023020206283540600_btx280-B41","doi-asserted-by":"crossref","first-page":"D428","DOI":"10.1093\/nar\/gki072","article-title":"Reactome: a knowledgebase of biological pathways","volume":"33","author":"Joshi-Tope","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B42","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B43","doi-asserted-by":"crossref","first-page":"11667","DOI":"10.1073\/pnas.0904715106","article-title":"Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression","volume":"106","author":"Khalil","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020206283540600_btx280-B44","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/ng1536","article-title":"Combinatorial microRNA target predictions","volume":"37","author":"Krek","year":"2005","journal-title":"Nat. Genet"},{"key":"2023020206283540600_btx280-B45","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1093\/bioinformatics\/btm563","article-title":"Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R","volume":"24","author":"Langfelder","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020206283540600_btx280-B46","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020206283540600_btx280-B47","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":"Lewis","year":"2005","journal-title":"Cell"},{"key":"2023020206283540600_btx280-B48","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B49","doi-asserted-by":"crossref","first-page":"3864","DOI":"10.1093\/nar\/gkq1348","article-title":"Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network","volume":"39","author":"Liao","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B50","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020206283540600_btx280-B51","doi-asserted-by":"crossref","first-page":"3873","DOI":"10.1093\/nar\/gkv255","article-title":"Modeling the relationship of epigenetic modifications to transcription factor binding","volume":"43","author":"Liu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B52","doi-asserted-by":"crossref","first-page":"2158","DOI":"10.1039\/C4MB00663A","article-title":"Mutated genes and driver pathways involved in myelodysplastic syndromes-a transcriptome sequencing based approach","volume":"11","author":"Liu","year":"2015","journal-title":"Mol. bioSystems"},{"key":"2023020206283540600_btx280-B53","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/nm0110-30","article-title":"Myelodysplasia: battle in the bone marrow","volume":"16","author":"Liu","year":"2010","journal-title":"Nat. Med"},{"key":"2023020206283540600_btx280-B54","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.710","article-title":"Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells","volume":"42","author":"Loewer","year":"2010","journal-title":"Nat. Genet"},{"key":"2023020206283540600_btx280-B55","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1111\/j.1365-2141.2012.09118.x","article-title":"Aberrant expression of MIR9 indicates poor prognosis in acute myeloid leukaemia","volume":"158","author":"Maki","year":"2012","journal-title":"Br. J. Haematol"},{"key":"2023020206283540600_btx280-B56","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1182\/blood-2008-10-187203","article-title":"Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome","volume":"114","author":"Mills","year":"2009","journal-title":"Blood"},{"key":"2023020206283540600_btx280-B57","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1089\/152791601750294344","article-title":"BioCarta","volume":"2","author":"Nishimura","year":"2004","journal-title":"Biotechnol. Softw. Internet Rep"},{"key":"2023020206283540600_btx280-B58","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/sj.leu.2404057","article-title":"Frequent elevation of Akt kinase phosphorylation in blood marrow and peripheral blood mononuclear cells from high-risk myelodysplastic syndrome patients","volume":"20","author":"Nyakern","year":"2006","journal-title":"Leukemia"},{"key":"2023020206283540600_btx280-B59","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.1182\/blood.V96.12.3932","article-title":"The role of apoptosis, proliferation, and the Bcl-2-related proteins in the myelodysplastic syndromes and acute myeloid leukemia secondary to MDS","volume":"96","author":"Parker","year":"2000","journal-title":"Blood"},{"key":"2023020206283540600_btx280-B60","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1182\/blood-2005-12-4769","article-title":"Gene expression profiles of CD34+ cells in myelodysplastic syndromes: involvement of interferon-stimulated genes and correlation to FAB subtype and karyotype","volume":"108","author":"Pellagatti","year":"2006","journal-title":"Blood"},{"key":"2023020206283540600_btx280-B61","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1101\/gr.6036807","article-title":"Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs","volume":"17","author":"Ponjavic","year":"2007","journal-title":"Genome Res"},{"key":"2023020206283540600_btx280-B62","doi-asserted-by":"crossref","first-page":"2985","DOI":"10.3748\/wjg.v19.i20.2985","article-title":"Role of microRNAs in the immune system, inflammation and cancer","volume":"19","author":"Raisch","year":"2013","journal-title":"World J. Gastroenterol"},{"key":"2023020206283540600_btx280-B63","doi-asserted-by":"crossref","first-page":"e00762","DOI":"10.7554\/eLife.00762","article-title":"A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics","volume":"2","author":"Rapicavoli","year":"2013","journal-title":"Elife"},{"key":"2023020206283540600_btx280-B64","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/leu.2011.221","article-title":"Deregulation of microRNAs in myelodysplastic syndrome","volume":"26","author":"Rhyasen","year":"2012","journal-title":"Leukemia"},{"key":"2023020206283540600_btx280-B65","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1146\/annurev-biochem-051410-092902","article-title":"Genome regulation by long noncoding RNAs","volume":"81","author":"Rinn","year":"2012","journal-title":"Annu. Rev. Biochem"},{"key":"2023020206283540600_btx280-B66","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","article-title":"A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?","volume":"146","author":"Salmena","year":"2011","journal-title":"Cell"},{"key":"2023020206283540600_btx280-B67","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the Pathway Interaction Database","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B68","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/ng0895-436","article-title":"Recurrent rearrangements in the high mobility group protein gene, HMGI-C, in benign mesenchymal tumours","volume":"10","author":"Schoenmakers","year":"1995","journal-title":"Nat. Genet"},{"key":"2023020206283540600_btx280-B69","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/leu.2011.151","article-title":"MicroRNAs in acute leukemia: from biological players to clinical contributors","volume":"26","author":"Schotte","year":"2012","journal-title":"Leukemia"},{"key":"2023020206283540600_btx280-B70","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/carcin\/bgn009","article-title":"Gab1 but not Grb2 mediates tumor progression in Met overexpressing colorectal cancer cells","volume":"29","author":"Seiden-Long","year":"2008","journal-title":"Carcinogenesis"},{"key":"2023020206283540600_btx280-B71","doi-asserted-by":"crossref","first-page":"4577","DOI":"10.1038\/onc.2011.621","article-title":"Long non-coding RNAs and cancer: a new frontier of translational research?","volume":"31","author":"Spizzo","year":"2012","journal-title":"Oncogene"},{"key":"2023020206283540600_btx280-B72","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1182\/blood-2005-03-1183","article-title":"The JAK2 V617F activating tyrosine kinase mutation is an infrequent event in both \u2018atypical\u2019 myeloproliferative disorders and myelodysplastic syndromes","volume":"106","author":"Steensma","year":"2005","journal-title":"Blood"},{"key":"2023020206283540600_btx280-B73","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1038\/ni.1945","article-title":"The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes","volume":"11","author":"Stittrich","year":"2010","journal-title":"Nat. Immunol"},{"key":"2023020206283540600_btx280-B74","doi-asserted-by":"crossref","first-page":"1370","DOI":"10.1093\/nar\/gkv020","article-title":"RPI-Pred: predicting ncRNA\u2013protein interaction using sequence and structural information","volume":"43","author":"Suresh","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B75","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/1476-4598-10-141","article-title":"Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer","volume":"10","author":"Tahira","year":"2011","journal-title":"Mol. Cancer"},{"key":"2023020206283540600_btx280-B76","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1007\/s12032-009-9264-2","article-title":"MicroRNA-9 reduces cell invasion and E-cadherin secretion in SK-Hep-1 cell","volume":"27","author":"Tan","year":"2010","journal-title":"Med. Oncol"},{"key":"2023020206283540600_btx280-B77","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.cell.2007.01.003","article-title":"FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress","volume":"128","author":"Tothova","year":"2007","journal-title":"Cell"},{"key":"2023020206283540600_btx280-B78","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"Trapnell","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023020206283540600_btx280-B79","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020206283540600_btx280-B80","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol"},{"key":"2023020206283540600_btx280-B81","doi-asserted-by":"crossref","first-page":"e1000641","DOI":"10.1371\/journal.pcbi.1000641","article-title":"Associating genes and protein complexes with disease via network propagation","volume":"6","author":"Vanunu","year":"2010","journal-title":"PLoS Comput. Biol"},{"key":"2023020206283540600_btx280-B82","doi-asserted-by":"crossref","first-page":"e79118","DOI":"10.1371\/journal.pone.0079118","article-title":"Discovering transcription and splicing networks in myelodysplastic syndromes","volume":"8","author":"Wang","year":"2013","journal-title":"PloS One"},{"key":"2023020206283540600_btx280-B83","doi-asserted-by":"crossref","first-page":"173.","DOI":"10.1186\/1476-4598-12-173","article-title":"Epigenetic inactivation of miR-9 family microRNAs in chronic lymphocytic leukemia\u2013implications on constitutive activation of NFkappaB pathway","volume":"12","author":"Wang","year":"2013","journal-title":"Mol. Cancer"},{"key":"2023020206283540600_btx280-B150","doi-asserted-by":"crossref","first-page":"3478","DOI":"10.1093\/nar\/gkv233","article-title":"Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B84","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1002\/hep.26361","article-title":"Long noncoding RNAs associated with liver regeneration 1 accelerates hepatocyte proliferation during liver regeneration by activating Wnt\/beta-catenin signaling","volume":"58","author":"Xu","year":"2013","journal-title":"Hepatology"},{"key":"2023020206283540600_btx280-B85","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.1126\/science.1151526","article-title":"Induced pluripotent stem cell lines derived from human somatic cells","volume":"318","author":"Yu","year":"2007","journal-title":"Science"},{"key":"2023020206283540600_btx280-B86","doi-asserted-by":"crossref","first-page":"D196","DOI":"10.1093\/nar\/gkv1273","article-title":"deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data","volume":"44","author":"Zheng","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020206283540600_btx280-B87","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/nature12308","article-title":"Temporal regulation of EGF signalling networks by the scaffold protein Shc1","volume":"499","author":"Zheng","year":"2013","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2622\/49041299\/bioinformatics_33_17_2622.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2622\/49041299\/bioinformatics_33_17_2622.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T04:09:03Z","timestamp":1750219743000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/17\/2622\/3796389"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,4]]},"references-count":88,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2017,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx280","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,9,1]]},"published":{"date-parts":[[2017,5,4]]}}}