Computational prediction and analysis of histone H3k27me1-associated miRNAs
Tài liệu tham khảo
Bannister, 2005, Reversing histone methylation, Nature, 436, 1103, 10.1038/nature04048
Jacob, 2009, H3K27me1 is E(z) in animals, but not in plants, Epigenetics, 4, 366, 10.4161/epi.4.6.9713
Chammas, 2020, Engaging chromatin: PRC2 structure meets function, Br. J. Cancer, 122, 315, 10.1038/s41416-019-0615-2
Rogenhofer, 2012, Global histone H3 lysine 27 (H3K27) methylation levels and their prognostic relevance in renal cell carcinoma, BJU Int., 109, 459, 10.1111/j.1464-410X.2011.10278.x
Ellinger, 2012, Global histone H3K27 methylation levels are different in localized and metastatic prostate cancer, Cancer Investig., 30, 92, 10.3109/07357907.2011.636117
Steiner, 2011, Patterns of histone H3 lysine 27 monomethylation and erythroid cell type-specific gene expression, J. Biol. Chem., 286, 39457, 10.1074/jbc.M111.243006
Kim, 2018, H3K27me1 is essential for MMP-9-dependent H3N-terminal tail proteolysis during osteoclastogenesis, Epigenetics Chromatin, 11, 23, 10.1186/s13072-018-0193-1
Tutar, 2014, miRNA and cancer; computational and experimental approaches, Curr. Pharm. Biotechnol., 15, 429, 10.2174/138920101505140828161335
Le, 2013, Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation, Bioinformatics, 29, i89, 10.1093/bioinformatics/btt231
Eulalio, 2008, Getting to the root of miRNA-mediated gene silencing, Cell, 132, 9, 10.1016/j.cell.2007.12.024
Ferland-McCollough, 2010, The involvement of microRNAs in type 2 diabetes, Biochem. Soc. Trans., 38, 1565, 10.1042/BST0381565
Farazi, 2011, miRNAs in human cancer, J. Pathol., 223, 102, 10.1002/path.2806
Port, 2010, Role of microRNAs in cardiovascular disease: therapeutic challenges and potentials, J. Cardiovasc. Pharmacol., 56, 444, 10.1097/FJC.0b013e3181f605b6
Qu, 2011, Circulating miRNAs: promising biomarkers of human cancer, Asian Pac. J. Cancer Prev., 12, 1117
Adai, 2005, Computational prediction of miRNAs in Arabidopsis thaliana, Genome Res., 15, 78, 10.1101/gr.2908205
Stegmayer, 1654, Computational prediction of novel miRNAs from genome-wide data, Methods Mol. Biol., 2017, 29
Grundhoff, 2011, Computational prediction of viral miRNAs, Methods Mol. Biol., 721, 143, 10.1007/978-1-61779-037-9_8
Mishra, 2011, miRNA prediction using computational approach, Adv. Exp. Med. Biol., 696, 75, 10.1007/978-1-4419-7046-6_8
Lin, 2020, RNAInter in 2020: RNA interactome repository with increased coverage and annotation, Nucleic Acids Res., 48, D189, 10.1093/nar/gkz804
Zhou, 2017, ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data, Nucleic Acids Res., 45, D43, 10.1093/nar/gkw965
Landgraf, 2007, A mammalian microRNA expression atlas based on small RNA library sequencing, Cell, 129, 1401, 10.1016/j.cell.2007.04.040
Kozomara, 2019, miRBase: from microRNA sequences to function, Nucleic Acids Res., 47, D155, 10.1093/nar/gky1141
Breiman, 2001, Random forests, Mach. Learn., 45, 5, 10.1023/A:1010933404324
Liaw, 2007
Belgiu, 2016, Random forest in remote sensing: a review of applications and future directions, ISPRS J. Photogramm. Remote Sens., 114, 24, 10.1016/j.isprsjprs.2016.01.011
Kern, 2020, miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems, Nucleic Acids Res., 10.1093/nar/gkaa309
Backes, 2016, miEAA: microRNA enrichment analysis and annotation, Nucleic Acids Res., 44, W110, 10.1093/nar/gkw345
Tong, 2019, TransmiR v2.0: an updated transcription factor-microRNA regulation database, Nucleic Acids Res., 47, D253, 10.1093/nar/gky1023
Stockley, 2013, Enrichment of FLI1 and RUNX1 mutations in families with excessive bleeding and platelet dense granule secretion defects, Blood, 122, 4090, 10.1182/blood-2013-06-506873
Saultier, 2017, Macrothrombocytopenia and dense granule deficiency associated with FLI1 variants: ultrastructural and pathogenic features, Haematologica, 102, 1006, 10.3324/haematol.2016.153577
Yates, 2019, Ensembl 2020, Nucleic Acids Res., 48, D682
Uhlen, 2015, Proteomics. Tissue-based map of the human proteome, Science, 347, 1260419, 10.1126/science.1260419
UniProt Consortium T, 2018, UniProt: the universal protein knowledgebase, Nucleic Acids Res., 46, 2699, 10.1093/nar/gky092
Brutsch, 2010, Integrin cytoplasmic domain-associated protein-1 attenuates sprouting angiogenesis, Circ. Res., 107, 592, 10.1161/CIRCRESAHA.110.217257
Qi, 2010, Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development, Nature, 466, 503, 10.1038/nature09261
Fortschegger, 2010, PHF8 targets histone methylation and RNA polymerase II to activate transcription, Mol. Cell. Biol., 30, 3286, 10.1128/MCB.01520-09
Nakagawa, 2000, Members of the HRT family of basic helix-loop-helix proteins act as transcriptional repressors downstream of Notch signaling, Proc. Natl. Acad. Sci. U. S. A., 97, 13655, 10.1073/pnas.250485597
Chen, 2017, Methyltransferase SETD2-mediated methylation of STAT1 Is critical for interferon antiviral activity, Cell, 170, 10.1016/j.cell.2017.06.042
Markert, 2008, The La-related protein LARP7 is a component of the 7SK ribonucleoprotein and affects transcription of cellular and viral polymerase II genes, EMBO Rep., 9, 569, 10.1038/embor.2008.72
Zhou, 2004, Coordination of transcription factor phosphorylation and histone methylation by the P-TEFb kinase during human immunodeficiency virus type 1 transcription, J. Virol., 78, 13522, 10.1128/JVI.78.24.13522-13533.2004
Vlachos, 2015, DIANA-miRPath v3.0: deciphering microRNA function with experimental support, Nucleic Acids Res., 43, W460, 10.1093/nar/gkv403
The Gene Ontology C, 2019, The gene ontology resource: 20 years and still GOing strong, Nucleic Acids Res., 47, D330, 10.1093/nar/gky1055
Ashburner, 2000, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat. Genet., 25, 25, 10.1038/75556
Kanehisa, 2013, Data, information, knowledge and principle: back to metabolism in KEGG, Nucleic Acids Res., 42, D199, 10.1093/nar/gkt1076
Vlachos, 2014, DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions, Nucleic Acids Res., 43, D153, 10.1093/nar/gku1215
Reczko, 2012, Functional microRNA targets in protein coding sequences, Bioinformatics, 28, 771, 10.1093/bioinformatics/bts043
Paraskevopoulou, 2013, DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows, Nucleic Acids Res., 41, W169, 10.1093/nar/gkt393
Agarwal, 2015, Predicting effective microRNA target sites in mammalian mRNAs, eLife, 4, 10.7554/eLife.05005
Johnston, 2003, Molecular mechanisms of insulin receptor substrate protein-mediated modulation of insulin signalling, FEBS Lett., 546, 32, 10.1016/S0014-5793(03)00438-1