C-It-Loci: A knowledge database for tissue-enriched loci

Bioinformatics

Volumn 31, Issue 21, 2015, Pages 3537-3543

  Weirick, Tyler ^a,b   John, David ^a,b   Dimmeler, Stefanie ^a,b   Uchida, Shizuka ^a,b  

^a GOETHE UNIVERSITY   (Germany)

^b German Centre of Cardiovascular Research (DZHK) Partner Site RheinMain   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; UNTRANSLATED RNA;

ANIMAL; ANTIBODY SPECIFICITY; CHEMISTRY; GENE LOCUS; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; KNOWLEDGE BASE; METABOLISM; MOUSE; SEQUENCE ANALYSIS; ZEBRA FISH;

ANIMALS; DATABASES, GENETIC; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KNOWLEDGE BASES; MICE; ORGAN SPECIFICITY; PROTEINS; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; ZEBRAFISH;

EID: 84947553244     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv410     Document Type: Article

References (36)

1. Ashburner,M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
2. Batzoglou,S. et al. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res., 10, 950-958.
3. Bejerano,G. et al. (2004) Ultraconserved elements in the human genome. Science (New York, N.Y.), 304, 1321-1325.
4. Bolstad,B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England), 19, 185-193.
5. Cabili,M.N. et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes. Dev., 25, 1915-1927.
6. Carninci,P. et al. (2005) The transcriptional landscape of the mammalian genome. Science (New York, N.Y.), 309, 1559-1563.
7. Chan,W.L. et al. (2014) lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. Comput. Biol. Chem., 50, 41-49.
8. Derrien,T. et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res., 22, 1775-1789.
9. Dimitrieva,S. and Bucher,P. (2013) UCNEbase - a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res., 41, D101-D109.
10. Eisenberg,E. and Levanon,E.Y. (2013) Human housekeeping genes, revisited. Trends Genet. TIG, 29, 569-574.
11. ENCODE Project Consortium,E.P. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
12. Engstrom,P.G. et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods, 10, 1185-1191.
13. Flicek,P. et al. (2014) Ensembl 2014. Nucleic Acids Res., 42, D749-D755.
14. Gellert,P. et al. (2010) C-It: a knowledge database for tissue-enriched genes. Bioinformatics (Oxford, England), 26, 2328-2333.
15. Gellert,P. et al. (2013) Noncoder: a web interface for exon array-based detection of long non-coding RNAs. Nucleic Acids Res., 41, e20.
16. Guttman,M. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
17. Johnsson,P. et al. (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochimica et Biophysica Acta, 1840, 1063-1071.
18. Kodama,Y. et al. (2012) The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res., 40, D54-D56.
19. Lander,E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
20. Landt,S.G. et al. (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res., 22, 1813-1831.
21. Maston,G.A. et al. (2006) Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet., 7, 29-59.
22. McWilliam,H. et al. (2013) Analysis tool web services from the EMBL-EBI. Nucleic Acids Res., 41, W597-W600.
23. Mortazavi,A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
24. Park,C. et al. (2014) lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. Bioinformatics (Oxford, England), 30, 2480-2485.
25. Pearson,W.R. et al. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
26. Pennacchio,L.A. et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature, 444, 499-502.
27. Qureshi,I.A. and Mehler,M.F. (2013) Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy. Neurotherapeutics J. Am. Soc. Exp. NeuroTherapeutics, 10, 632-646.
28. Sanyal,A. et al. (2012) The long-range interaction landscape of gene promoters. Nature, 489, 109-113.
29. Tang,J.Y. et al. (2013) Long noncoding RNAs-related diseases, cancers, and drugs. TheScientificWorldJournal, 2013, 943539.
30. Uchida,S. and Dimmeler,S. (2015) Long noncoding RNAs in cardiovascular diseases. Circ. Res., 116, 737-750.
31. Uchida,S. et al. (2012) Deeply dissecting stemness: making sense to non-coding RNAs in stem cells. Stem Cell Rev., 8, 78-86.
32. Visel,A. et al. (2007) VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res., 35, D88-D92.
33. Volders,P.J. et al. (2015) An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res., 43, D174-D180.
34. Xie,C. et al. (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res., 42, D98-D103.
35. Yates,A. et al. (2015) The Ensembl REST API: Ensembl data for any language. Bioinformatics (Oxford, England), 31, 143-145.
36. Zhao,H. et al. (2014) CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics (Oxford, England), 30, 1006-1007.