The RNA editing landscape in acute myeloid leukemia reveals associations with disease mutations and clinical outcome
Tài liệu tham khảo
Ferrara, 2013, Acute myeloid leukaemia in adults, Lancet, 381, 484, 10.1016/S0140-6736(12)61727-9
Goldman, 2019, Epigenetic modifications in acute myeloid leukemia: prognosis, treatment, and heterogeneity, Front. Genet., 10, 133, 10.3389/fgene.2019.00133
Gallipoli, 2015, Epigenetic regulators as promising therapeutic targets in acute myeloid leukemia, Ther. Adv. Hematol., 6, 103, 10.1177/2040620715577614
Nishikura, 2010, Functions and regulation of RNA editing by ADAR deaminases, Annu. Rev. Biochem., 79, 321, 10.1146/annurev-biochem-060208-105251
Picardi, 2017, REDIportal: a comprehensive database of A-to-I RNA editing events in humans, Nucleic Acids Res., 45, D750, 10.1093/nar/gkw767
Ramaswami, 2014, RADAR: a rigorously annotated database of A-to-I RNA editing, Nucleic Acids Res., 42, D109, 10.1093/nar/gkt996
Kiran, 2010, DARNED: a DAtabase of RNa EDiting in humans, Bioinformatics, 26, 1772, 10.1093/bioinformatics/btq285
Tan, 2017, Dynamic landscape and regulation of RNA editing in mammals, Nature, 550, 249, 10.1038/nature24041
Han, 2015, The genomic landscape and clinical relevance of A-to-I RNA editing in human cancers, Cancer Cell, 28, 515, 10.1016/j.ccell.2015.08.013
Peng, 2018, A-to-I RNA editing contributes to proteomic diversity in cancer, Cancer Cell, 33, 817, 10.1016/j.ccell.2018.03.026
Paz-Yaacov, 2015, Elevated RNA editing activity is a major contributor to transcriptomic diversity in tumors, Cell Rep., 13, 267, 10.1016/j.celrep.2015.08.080
Silvestris, 2019, Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma, Genome Biol., 20, 33, 10.1186/s13059-019-1647-x
Beghini, 2000, RNA hyperediting and alternative splicing of hematopoietic cell phosphatase (PTPN6) gene in acute myeloid leukemia, Hum. Mol. Genet., 9, 2297, 10.1093/oxfordjournals.hmg.a018921
Rossetti, 2017, RNA editing signature during myeloid leukemia cell differentiation, Leukemia, 31, 2824, 10.1038/leu.2017.134
Chan, 2020, RNA editing in cancer impacts mRNA abundance in immune response pathways, Genome Biol., 21, 268, 10.1186/s13059-020-02171-4
Tyner, 2018, Functional genomic landscape of acute myeloid leukaemia, Nature, 562, 526, 10.1038/s41586-018-0623-z
Ley, 2013, Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia, N. Engl. J. Med., 368, 2059, 10.1056/NEJMoa1301689
Tzelepis, 2016, A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia, Cell Rep., 17, 1193, 10.1016/j.celrep.2016.09.079
Roth, 2019, Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity, Nat. Methods, 16, 1131, 10.1038/s41592-019-0610-9
Guo, 2021, ADAR2-repressed RNA editing: a novel mechanism contributing to t (8:21) AML leukemogenesis, bioRxiv
Papaemmanuil, 2016, Genomic classification and prognosis in acute myeloid leukemia, N. Engl. J. Med., 374, 2209, 10.1056/NEJMoa1516192
Therneau, 2000
Zhang, 2020, Long noncoding RNA SOCS2-AS promotes leukemogenesis in FLT3-ITD+ acute myeloid leukemia through miRNA-221, OncoTargets Ther., 13, 2925, 10.2147/OTT.S222734
Venugopal, 2020, JAKs to STATs: a tantalizing therapeutic target in acute myeloid leukemia, Blood Rev., 40, 10.1016/j.blre.2019.100634
Lappalainen, 2013, Transcriptome and genome sequencing uncovers functional variation in humans, Nature, 501, 506, 10.1038/nature12531
Zhao, 2013, GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data, Genome Biol., 14, R74, 10.1186/gb-2013-14-7-r74
Degner, 2012, DNase I sensitivity QTLs are a major determinant of human expression variation, Nature, 482, 390, 10.1038/nature10808
Ramaswami, 2015, Genetic mapping uncovers cis-regulatory landscape of RNA editing, Nat. Commun., 6, 8194, 10.1038/ncomms9194
Breen, 2019, Global landscape and genetic regulation of RNA editing in cortical samples from individuals with schizophrenia, Nat. Neurosci., 22, 1402, 10.1038/s41593-019-0463-7
McCarthy, 2016, A reference panel of 64, 976 haplotypes for genotype imputation, Nat. Genet., 48, 1279, 10.1038/ng.3643
Josse, 2016, missMDA: a package for handling missing values in multivariate data analysis, J. Stat. Softw., 70
Song, 2011, Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity, Genome Res., 21, 1757, 10.1101/gr.121541.111
Bartonicek, 2017, Intergenic disease-associated regions are abundant in novel transcripts, Genome Biol., 18, 241, 10.1186/s13059-017-1363-3
2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247
Thurman, 2012, The accessible chromatin landscape of the human genome, Nature, 489, 75, 10.1038/nature11232
Breeze, 2022, Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations, Genome Biol., 23, 13, 10.1186/s13059-021-02560-3
Moore, 2020, Expanded encyclopaedias of DNA elements in the human and mouse genomes, Nature, 583, 699, 10.1038/s41586-020-2493-4
Porath, 2017, Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance, Genome Biol., 18, 185, 10.1186/s13059-017-1315-y
Chen, 2013, Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma, Nat. Med., 19, 209, 10.1038/nm.3043
Quinones-Valdez, 2019, Regulation of RNA editing by RNA-binding proteins in human cells, Commun. Biol., 2, 19, 10.1038/s42003-018-0271-8
Xiao, 2019, Pervasive chromatin-RNA binding protein interactions enable RNA-based regulation of transcription, Cell, 178, 107, 10.1016/j.cell.2019.06.001
McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110
Wang, 2010, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Res., 38, e164, 10.1093/nar/gkq603
Jun, 2015, An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data, Genome Res., 25, 918, 10.1101/gr.176552.114
Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616
Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8
Delaneau, 2017, A complete tool set for molecular QTL discovery and analysis, Nat. Commun., 8, 10.1038/ncomms15452
Grossman, 2016, Toward a shared vision for cancer genomic data, N. Engl. J. Med., 375, 1109, 10.1056/NEJMp1607591
Auton, 2015, A global reference for human genetic variation, Nature, 526, 68, 10.1038/nature15393
Piskol, 2013, Reliable identification of genomic variants from RNA-seq data, Am. J. Hum. Genet., 93, 641, 10.1016/j.ajhg.2013.08.008
Bazak, 2014, Genome-wide analysis of Alu editability, Nucleic Acids Res., 42, 6876, 10.1093/nar/gku414
Anders, 2015, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638
Coleman, 2016, Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray, Brief. Funct. Genomics, 15, 298, 10.1093/bfgp/elv037
Fort, 2017, MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets, Bioinformatics, 33, 1895, 10.1093/bioinformatics/btx074
Storey, 2003, Statistical significance for genomewide studies, Proc. Natl. Acad. Sci. USA, 100, 9440, 10.1073/pnas.1530509100
Robinson, 2010, A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biol., 11, R25, 10.1186/gb-2010-11-3-r25
Consortium, 2017, Genetic effects on gene expression across human tissues, Nature, 550, 204, 10.1038/nature24277
Gel, 2016, regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests, Bioinformatics, 32, 289, 10.1093/bioinformatics/btv562
