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Volumn 6, Issue , 2016, Pages

ANGIOGENES: Knowledge database for protein-coding and noncoding RNA genes in endothelial cells

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; TRANSCRIPTOME;

EID: 84984873720     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep32475     Document Type: Article
Times cited : (25)

References (48)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921, doi: 10.1038/35057062 (2001).
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 2
    • 84924134321 scopus 로고    scopus 로고
    • Long Noncoding RNAs in cardiovascular diseases
    • Uchida, S. & Dimmeler, S. Long Noncoding RNAs in Cardiovascular Diseases. Circulation research 116, 737-750, doi: 10.1161/circresaha.116.302521 (2015).
    • (2015) Circulation Research , vol.116 , pp. 737-750
    • Uchida, S.1    Dimmeler, S.2
  • 3
    • 84857647159 scopus 로고    scopus 로고
    • Deeply dissecting stemness: Making sense to non-coding RNAs in stem cells
    • Uchida, S., Gellert, P. & Braun, T. Deeply dissecting stemness: making sense to non-coding RNAs in stem cells. Stem cell reviews 8, 78-86, doi: 10.1007/s12015-011-9294-y (2012).
    • (2012) Stem Cell Reviews , vol.8 , pp. 78-86
    • Uchida, S.1    Gellert, P.2    Braun, T.3
  • 4
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annual review of biochemistry 81, 145-166, doi: 10.1146/annurev-biochem-051410-092902 (2012).
    • (2012) Annual Review of Biochemistry , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 5
    • 84891923027 scopus 로고    scopus 로고
    • Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs
    • Roberts, T. C., Morris, K. V. & Weinberg, M. S. Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs. Epigenetics 9, 13-20, doi: 10.4161/epi.26700 (2014).
    • (2014) Epigenetics , vol.9 , pp. 13-20
    • Roberts, T.C.1    Morris, K.V.2    Weinberg, M.S.3
  • 6
    • 84911444179 scopus 로고    scopus 로고
    • Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes
    • Ezkurdia, I. et al. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Human molecular genetics 23, 5866-5878, doi: 10.1093/hmg/ddu309 (2014).
    • (2014) Human Molecular Genetics , vol.23 , pp. 5866-5878
    • Ezkurdia, I.1
  • 7
    • 84855539848 scopus 로고    scopus 로고
    • Targeted RNA sequencing reveals the deep complexity of the human transcriptome
    • Mercer, T. R. et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nature biotechnology 30, 99-104, doi: 10.1038/nbt.2024 (2012).
    • (2012) Nature Biotechnology , vol.30 , pp. 99-104
    • Mercer, T.R.1
  • 8
    • 84928914391 scopus 로고    scopus 로고
    • ALDB: A domestic-animal long noncoding RNA database
    • Li, A. et al. ALDB: a domestic-animal long noncoding RNA database. Plos One 10, e0124003, doi: 10.1371/journal.pone.0124003 (2015).
    • (2015) Plos One , vol.10 , pp. e0124003
    • Li, A.1
  • 9
    • 84947553244 scopus 로고    scopus 로고
    • C-It-Loci: A knowledge database for tissue-enriched loci
    • Weirick, T., John, D., Dimmeler, S. & Uchida, S. C-It-Loci: a knowledge database for tissue-enriched loci. Bioinformatics (Oxford, England) 31, 3537-3543, doi: 10.1093/bioinformatics/btv410 (2015).
    • (2015) Bioinformatics (Oxford, England) , vol.31 , pp. 3537-3543
    • Weirick, T.1    John, D.2    Dimmeler, S.3    Uchida, S.4
  • 10
    • 84876566914 scopus 로고    scopus 로고
    • ChIPBase: A database for decoding the transcriptional regulation of long noncoding RNA and microRNA genes from ChIP-Seq data
    • Yang, J. H., Li, J. H., Jiang, S., Zhou, H. & Qu, L. H. ChIPBase: a database for decoding the transcriptional regulation of long noncoding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 41, D177-D187, doi: 10.1093/nar/gks1060 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. D177-D187
    • Yang, J.H.1    Li, J.H.2    Jiang, S.3    Zhou, H.4    Qu, L.H.5
  • 11
    • 84943156256 scopus 로고    scopus 로고
    • Co-LncRNA: Investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
    • Zhao, Z. et al. Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data. Database (Oxford) 2015, doi: 10.1093/database/bav082 (2015).
    • (2015) Database (Oxford) , vol.2015
    • Zhao, Z.1
  • 12
    • 84976909135 scopus 로고    scopus 로고
    • DeepBase v2.0: Identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data
    • Zheng, L. L. et al. DeepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. Nucleic Acids Res, doi: 10.1093/nar/gkv1273 (2015).
    • (2015) Nucleic Acids Res
    • Zheng, L.L.1
  • 13
    • 84876523096 scopus 로고    scopus 로고
    • DIANA-LncBase: Experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
    • Paraskevopoulou, M. D. et al. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res 41, D239-D245, doi: 10.1093/nar/gks1246 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. D239-D245
    • Paraskevopoulou, M.D.1
  • 14
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927, doi: 10.1101/gad.17446611 (2011).
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1
  • 15
    • 84965186421 scopus 로고    scopus 로고
    • LncRNA2Function: A comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
    • Jiang, Q. et al. LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics 16 Suppl 3, S2, doi: 10.1186/1471-2164-16-s3-s2 (2015).
    • (2015) BMC Genomics , vol.16 , pp. S2
    • Jiang, Q.1
  • 16
    • 84946013175 scopus 로고    scopus 로고
    • LncRNAdb v2.0: Expanding the reference database for functional long noncoding RNAs
    • Quek, X. C. et al. LncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 43, D168-D173, doi: 10.1093/nar/gku988 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D168-D173
    • Quek, X.C.1
  • 17
    • 84902279606 scopus 로고    scopus 로고
    • LncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome
    • Chan, W. L., Huang, H. D. & Chang, J. G. LncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. Computational biology and chemistry 50, 41-49, doi: 10.1016/j.compbiolchem.2014.01.003 (2014).
    • (2014) Computational Biology and Chemistry , vol.50 , pp. 41-49
    • Chan, W.L.1    Huang, H.D.2    Chang, J.G.3
  • 18
    • 84907032373 scopus 로고    scopus 로고
    • LncRNAtor: A comprehensive resource for functional investigation of long non-coding RNAs
    • Park, C., Yu, N., Choi, I., Kim, W. & Lee, S. LncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. Bioinformatics (Oxford, England) 30, 2480-2485, doi: 10.1093/bioinformatics/btu325 (2014).
    • (2014) Bioinformatics (Oxford, England) , vol.30 , pp. 2480-2485
    • Park, C.1    Yu, N.2    Choi, I.3    Kim, W.4    Lee, S.5
  • 19
    • 85015966988 scopus 로고    scopus 로고
    • MTD: A mammalian transcriptomic database to explore gene expression and regulation
    • Sheng, X. et al. MTD: a mammalian transcriptomic database to explore gene expression and regulation. Brief Bioinform, doi: 10.1093/bib/bbv117 (2016).
    • (2016) Brief Bioinform
    • Sheng, X.1
  • 20
    • 84976892806 scopus 로고    scopus 로고
    • NONCODE 2016: An informative and valuable data source of long non-coding RNAs
    • Zhao, Y. et al. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res, doi: 10.1093/nar/gkv1252 (2015).
    • (2015) Nucleic Acids Res
    • Zhao, Y.1
  • 21
    • 58149177177 scopus 로고    scopus 로고
    • NRED: A database of long noncoding RNA expression
    • Dinger, M. E. et al. NRED: a database of long noncoding RNA expression. Nucleic Acids Res. 37, D122-D126, doi: 10.1093/nar/gkn617 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. D122-D126
    • Dinger, M.E.1
  • 22
    • 84942909779 scopus 로고    scopus 로고
    • TANRIC: An interactive open platform to explore the function of lncRNAs in cancer
    • Li, J. et al. TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer. Cancer Res. 75, 3728-3737, doi: 10.1158/0008-5472.can-15-0273 (2015).
    • (2015) Cancer Res. , vol.75 , pp. 3728-3737
    • Li, J.1
  • 23
    • 84897833980 scopus 로고    scopus 로고
    • TF2LncRNA: Identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data
    • Jiang, Q. et al. TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data. Biomed Res Int. 2014, 317642, doi: 10.1155/2014/317642 (2014).
    • (2014) Biomed Res Int. , vol.2014 , pp. 317642
    • Jiang, Q.1
  • 24
    • 84891798006 scopus 로고    scopus 로고
    • NONCODEv4: Exploring the world of long non-coding RNA genes
    • Xie, C. et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic acids research 42, D98-103, doi: 10.1093/nar/gkt1222 (2014).
    • (2014) Nucleic Acids Research , vol.42 , pp. D98-D103
    • Xie, C.1
  • 25
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research 22, 1775-1789, doi: 10.1101/gr.132159.111 (2012).
    • (2012) Genome Research , vol.22 , pp. 1775-1789
    • Derrien, T.1
  • 26
    • 84877575447 scopus 로고    scopus 로고
    • Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo
    • Ramos, A. D. et al. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12, 616-628, doi: 10.1016/j.stem.2013.03.003 (2013).
    • (2013) Cell Stem Cell , vol.12 , pp. 616-628
    • Ramos, A.D.1
  • 27
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano, G. et al. Ultraconserved elements in the human genome. Science (New York, N.Y.) 304, 1321-1325, doi: 10.1126/science.1098119 (2004).
    • (2004) Science (New York, N.Y.) , vol.304 , pp. 1321-1325
    • Bejerano, G.1
  • 28
    • 84876541696 scopus 로고    scopus 로고
    • UCNEbase-A database of ultraconserved non-coding elements and genomic regulatory blocks
    • Dimitrieva, S. & Bucher, P. UCNEbase-a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic acids research 41, D101-D109, doi: 10.1093/nar/gks1092 (2013).
    • (2013) Nucleic Acids Research , vol.41 , pp. D101-D109
    • Dimitrieva, S.1    Bucher, P.2
  • 29
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502, doi: 10.1038/nature05295 (2006).
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1
  • 30
    • 33846112470 scopus 로고    scopus 로고
    • VISTA Enhancer Browser-A database of tissue-specific human enhancers
    • Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic acids research 35, D88-D92, doi: 10.1093/nar/gkl822 (2007).
    • (2007) Nucleic Acids Research , vol.35 , pp. D88-D92
    • Visel, A.1    Minovitsky, S.2    Dubchak, I.3    Pennacchio, L.A.4
  • 32
    • 77956180067 scopus 로고    scopus 로고
    • Identification of right heart-enriched genes in a murine model of chronic outflow tract obstruction
    • Kreymborg, K. et al. Identification of right heart-enriched genes in a murine model of chronic outflow tract obstruction. J Mol Cell Cardiol. 49, 598-605, doi: 10.1016/j.yjmcc.2010.07.014 (2010).
    • (2010) J Mol Cell Cardiol. , vol.49 , pp. 598-605
    • Kreymborg, K.1
  • 33
    • 62749116746 scopus 로고    scopus 로고
    • An integrated approach for the systematic identification and characterization of heart-enriched genes with unknown functions
    • Uchida, S. et al. An integrated approach for the systematic identification and characterization of heart-enriched genes with unknown functions. BMC Genomics 10, 100, doi: 10.1186/1471-2164-10-100 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 100
    • Uchida, S.1
  • 34
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhausser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342, doi: 10.1038/nature10098 (2011).
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhausser, B.1
  • 35
    • 84920269464 scopus 로고    scopus 로고
    • Proteomics. Tissue-based map of the human proteome
    • Uhlen, M. et al. Proteomics. Tissue-based map of the human proteome. Science (New York, N.Y.) 347, 1260419, doi: 10.1126/science.1260419 (2015).
    • (2015) Science (New York, N.Y.) , vol.347 , pp. 1260419
    • Uhlen, M.1
  • 36
    • 84860581983 scopus 로고    scopus 로고
    • Genome-wide analysis of long noncoding RNA stability
    • Clark, M. B. et al. Genome-wide analysis of long noncoding RNA stability. Genome research 22, 885-898, doi: 10.1101/gr.131037.111 (2012).
    • (2012) Genome Research , vol.22 , pp. 885-898
    • Clark, M.B.1
  • 37
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (New York, N.Y.) 308, 1149-1154, doi: 10.1126/science.1108625 (2005).
    • (2005) Science (New York, N.Y.) , vol.308 , pp. 1149-1154
    • Cheng, J.1
  • 38
    • 79959403670 scopus 로고    scopus 로고
    • Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
    • Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome research 21, 1160-1167, doi: 10.1101/gr.110882.110 (2011).
    • (2011) Genome Research , vol.21 , pp. 1160-1167
    • Islam, S.1
  • 39
    • 79960088946 scopus 로고    scopus 로고
    • Cell-to-cell variability of alternative RNA splicing
    • Waks, Z., Klein, A. M. & Silver, P. A. Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol 7, 506, doi: 10.1038/msb.2011.32 (2011).
    • (2011) Mol Syst Biol , vol.7 , pp. 506
    • Waks, Z.1    Klein, A.M.2    Silver, P.A.3
  • 40
    • 84941344454 scopus 로고    scopus 로고
    • Causal biological network database: A comprehensive platform of causal biological network models focused on the pulmonary and vascular systems
    • Boue, S. et al. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. Database (Oxford) 2015, bav030, doi: 10.1093/database/bav030 (2015).
    • (2015) Database (Oxford) , vol.2015 , pp. bav030
    • Boue, S.1
  • 41
    • 84856488426 scopus 로고    scopus 로고
    • A curated database of genetic markers from the angiogenesis/VEGF pathway and their relation to clinical outcome in human cancers
    • Savas, S. A curated database of genetic markers from the angiogenesis/VEGF pathway and their relation to clinical outcome in human cancers. Acta Oncol. 51, 243-246, doi: 10.3109/0284186x.2011.636758 (2012).
    • (2012) Acta Oncol. , vol.51 , pp. 243-246
    • Savas, S.1
  • 42
    • 84941094166 scopus 로고    scopus 로고
    • PubAngioGen: A database and knowledge for angiogenesis and related diseases
    • Li, P. et al. PubAngioGen: a database and knowledge for angiogenesis and related diseases. Nucleic acids research 43, D963-D967, doi: 10.1093/nar/gku1139 (2015).
    • (2015) Nucleic Acids Research , vol.43 , pp. D963-D967
    • Li, P.1
  • 43
    • 84867306721 scopus 로고    scopus 로고
    • Snakemake-A scalable bioinformatics workflow engine
    • Koster, J. & Rahmann, S. Snakemake-a scalable bioinformatics workflow engine. Bioinformatics (Oxford, England) 28, 2520-2522, doi: 10.1093/bioinformatics/bts480 (2012).
    • (2012) Bioinformatics (Oxford, England) , vol.28 , pp. 2520-2522
    • Koster, J.1    Rahmann, S.2
  • 44
    • 84862198590 scopus 로고    scopus 로고
    • The Sequence Read Archive: Explosive growth of sequencing data
    • Kodama, Y., Shumway, M. & Leinonen, R. The Sequence Read Archive: explosive growth of sequencing data. Nucleic acids research 40, D54-D56, doi: 10.1093/nar/gkr854 (2012).
    • (2012) Nucleic Acids Research , vol.40 , pp. D54-D56
    • Kodama, Y.1    Shumway, M.2    Leinonen, R.3
  • 45
    • 84883577718 scopus 로고    scopus 로고
    • Analysis Tool Web Services from the EMBL-EBI
    • McWilliam, H. et al. Analysis Tool Web Services from the EMBL-EBI. Nucleic acids research 41, W597-W600, doi: 10.1093/nar/gkt376 (2013).
    • (2013) Nucleic Acids Research , vol.41 , pp. W597-W600
    • McWilliam, H.1
  • 46
    • 85018771813 scopus 로고    scopus 로고
    • Resolving the problem of multiple accessions of the same transcript deposited across various public databases
    • Weirick, T., John, D. & Uchida, S. Resolving the problem of multiple accessions of the same transcript deposited across various public databases. Brief Bioinform, doi: 10.1093/bib/bbw017 (2016).
    • (2016) Brief Bioinform
    • Weirick, T.1    John, D.2    Uchida, S.3
  • 47
    • 84991401479 scopus 로고    scopus 로고
    • The identification and characterization of novel transcripts from RNA-seq data
    • Weirick, T. et al. The identification and characterization of novel transcripts from RNA-seq data. Brief Bioinform, doi: 10.1093/bib/bbv067 (2015).
    • (2015) Brief Bioinform
    • Weirick, T.1
  • 48
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The gene ontology consortium
    • Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25-29, doi: 10.1038/75556 (2000).
    • (2000) Nature Genetics , vol.25 , pp. 25-29
    • Ashburner, M.1


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