ncRNAppi A tool for identifying disease-related miRNA and siRNA targeting pathways

Bioinformatics

Volumn 25, Issue 23, 2009, Pages 3199-3201

  Ng, Ka Lok ^a   Liu, Hsueh Chuan ^b   Lee, Shan Chih ^c  

^a ASIA UNIVERSITY   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^c CHUNG SHAN MEDICAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; SMALL INTERFERING RNA;

ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; GENETIC DATABASE; GENOMICS; HUMAN; INTERNET; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOMICS; HUMANS; INTERNET; MICRORNAS; PROTEIN INTERACTION MAPPING; RNA, MESSENGER; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 75949129961     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp574     Document Type: Article

References (21)

1. Alfarano, C. et al. (2006) The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res., 33, D418-D424.
2. Amberger, J. et al. (2009) McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res., 37, D793-D796.
3. Breitkreutz, B.J. et al. (2008) The BioGRID interaction database: 2008 update. Nucleic Acids Res., 36, D637-D640.
4. Chan, H.-H. and Sun, H.S. (2006) Identification of novel tumor-associated gene (TAG) by bioinformatics analysis. MSc. Thesis, National Cheng Kung University, Taiwan.
5. Chatraryamontri, A. et al (2007). MINT: the molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
6. Esquela-Kerscher A. and Slack F.J. (2006). Oncomirs - microRNAs with a role in cancer. Nat. Rev. Cancer, 6, 259-269.
7. Gene Ontology Consortium (2006). The Gene Ontology (GO) project in 2006. Nucleic Acids Res., 34, D322-D326.
8. He, L. et al., (2005) A microRNA polycistron as a potential human oncogene. Nature, 435, 828-833.
9. Kanehisa, M. et al (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
10. Kerrien, S. et al. (2007) IntAct - open source resource for molecular interaction database. Nucleic Acids Res., 35, D561-D565.
11. Mewes, H.W. et al. (2008) MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res., 36, D196-D201.
12. Mishra, G.R. et al. (2006). Human protein reference database - 2006 update. Nucleic Acids Res., 34, D411-D414.
13. Nam, S. et al. (2008) miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res., 36, D159-D164.
14. Papadopoulos, G.L. et al. (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res., D155-D158.
15. Pontius, J.U. et al. (2003) UniGene: a unified view of the transcriptome. In The NCBI Handbook. Ch. 21, Edited by National Center for Biotechnology Information, Bethesda, MD.
16. Ren, Y. et al. (2006) siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics, 22, 1027-1028.
17. Salwinski, L. et al. (2004) The database of interacting proteins. Nucleic Acids Res., 32, D449-D451.
18. Sethupathy, P. et al. (2006) TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA, 12, 192-197.
19. Wang, X. (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA, 14, 1012-1017.
20. Xenarios, I. et al. (2002). DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
21. Zhang, W et al. (2007). MicroRNAs in tumorigenesis: a primer. Am. J. Pathol., 171, 728-738.