A study of Cancer-related MicroRNAs through Expression Data and Literature Search
MicroRNAs (miRNAs) are a class of non-coding
RNAs that hybridize to mRNAs and induce either translation
repression or mRNA cleavage. Recently, it has been reported that
miRNAs could possibly play an important role in human diseases. By
integrating miRNA target genes, cancer genes, miRNA and mRNA
expression profiles information, a database is developed to link
miRNAs to cancer target genes. The database provides experimentally
verified human miRNA target genes information, including oncogenes
and tumor suppressor genes. In addition, fragile sites information for
miRNAs, and the strength of the correlation of miRNA and its target
mRNA expression level for nine tissue types are computed, which
serve as an indicator for suggesting miRNAs could play a role in
human cancer. The database is freely accessible at
http://ppi.bioinfo.asia.edu.tw/mirna_target/index.html.
[1] Eric A Miska, How microRNAs control cell division, differentiation and
death. Current Opinion in Genetics & Development. 15(5), 563-568,
2005.
[2] V. Narry.Kim, MicroRNA biogenesis: coordinated cropping and dicing.
Nature Reviews. Molecular Cell Biology 6(5), 376-385, 2005.
[3] Erno Wienholds, and Ronald H.A. Plasterk,. MicroRNA function in
animal development. FEBS Letters, 579(26), 5911-5922, 2005.
[4] L.P. Lim, N.C. Lau, P. Garrett-Engele, A.Grimson, J.M Schelter., J.
Castle, D.P. Bartel, P.S. Linsley, J.M. Johnson. Microarray analysis
shows that some microRNAs downregulate large numbers of target
mRNAs. Nature, 433, 769-73, 2005.
[5] L.F. Sempere, S. Freemantle, I. Pitha-Rowe, E. Moss, E. Dmitrovsky, V.
Ambros. Expression profiling of mammalian microRNAs uncovers a
subset of brain-expressed microRNAs with possible roles in murine and
human neuronal differentiation. Genome Biol., 5, R13. 2004.
[6] L. He, J.M. Thomson, M.T. Hemann, E Hernando-Monge., D Mu., S.
Goodson, S. Powers, C. Cordon-Cardo, S.W. Lowe, G.J. Hannon, S.M.
Hammond. A microRNA polycistron as a potential human oncogene.
Nature, 435, 828-33, 2005.
[7] A. Esquela-Kerscher & F.J. Slack Oncomirs - microRNAs with a role in
cancer. Nat Rev Cancer 2006, 6(4):259-269, 2006.
[8] B Zhang, X Pan, GP Cobb, TA Anderson.. microRNAs as oncogenes and
tumor suppressors. Dev Biol. 302(1):1-12, 2007.
[9] P. Sethupathy, B. Corda and A.G Hatzigeorgiou., TarBase: A
comprehensive database of experimentally supported animal miRNA
targets, RNA, Vol. 12, pp.192-197, 2005.
[10] Shankavaram et al., Transcript and protein expression profiles of the
NCI-60 cancer cell panel: an integromic microarray study, Molecular
Cancer Therapeutics, Vol. 6, No. 3, pp.820-832, 2007
[11] Blower et. al., MiRNA expression profiles for the NCI-60 cancer cell
panel, Molecular Cancer Therapeutics, Vol. 6, No. 5, pp.1483-1491,
2007.
[12] Hsiang-Han.Chan and H. Sunny Sun, Identification of novel
tumor-associated gene (TAG) by bioinformatics analysis. Master Thesis,
Institute of Molecular Medicine, National Cheng Kung University, 2005.
[13] S Griffiths-Jones., Russell J. Grocock, Stijn van Dongen, Alex Bateman,
Anton J.Enright, miRBase: miRNA sequences, targets and gene
nomenclature, Nucleic Acids Research, Vol. 34, pp.140-144, 2006.
[14] Calin et al. Human microRNA genes are frequently located at fragile sites
and genomic regions involved in cancers. Proc Natl Acad Sci U S A,
101(9):2999-3004, 2004.
[15] Debacker Kim and R.Frank Kooy. Fragile sites and human disease.
Human Molecular Genetics, 16(2), R150-158, 2007.
[16] Kuan-Ting Lin, Chia-Hung Liu, Jen-Jie Chiou, Wen-Hsien Tseng,
Kuang-Lung Lin, Chun-Nan Hsu, Gene Name Service: No-Nonsense
Alias Resolution Service for Homo Sapiens Genes, Proceedings of the
2007 IEEE/WIC/ACM International Conferences on Web Intelligence
and Intelligent Agent Technology-Workshops, pp.185-188, 2007.
[17] A Cimmino et al.,. miR-15 and miR-16 induce apoptosis by targeting
BCL2. Proc Natl Acad Sci., 102(39):13944-9, 2005. Erratum in: Proc
Natl Acad Sci 14;103(7):2464, 2006..
[18] L Xia, D Zhang, R Du, Y Pan, L Zhao, S Sun, L Hong, J Liu, D Fan.
miR-15b and miR-16 modulate multidrug resistance by targeting BCL2 in
human gastric cancer cells. Int J Cancer. 123(2):372-9, 2008.
[1] Eric A Miska, How microRNAs control cell division, differentiation and
death. Current Opinion in Genetics & Development. 15(5), 563-568,
2005.
[2] V. Narry.Kim, MicroRNA biogenesis: coordinated cropping and dicing.
Nature Reviews. Molecular Cell Biology 6(5), 376-385, 2005.
[3] Erno Wienholds, and Ronald H.A. Plasterk,. MicroRNA function in
animal development. FEBS Letters, 579(26), 5911-5922, 2005.
[4] L.P. Lim, N.C. Lau, P. Garrett-Engele, A.Grimson, J.M Schelter., J.
Castle, D.P. Bartel, P.S. Linsley, J.M. Johnson. Microarray analysis
shows that some microRNAs downregulate large numbers of target
mRNAs. Nature, 433, 769-73, 2005.
[5] L.F. Sempere, S. Freemantle, I. Pitha-Rowe, E. Moss, E. Dmitrovsky, V.
Ambros. Expression profiling of mammalian microRNAs uncovers a
subset of brain-expressed microRNAs with possible roles in murine and
human neuronal differentiation. Genome Biol., 5, R13. 2004.
[6] L. He, J.M. Thomson, M.T. Hemann, E Hernando-Monge., D Mu., S.
Goodson, S. Powers, C. Cordon-Cardo, S.W. Lowe, G.J. Hannon, S.M.
Hammond. A microRNA polycistron as a potential human oncogene.
Nature, 435, 828-33, 2005.
[7] A. Esquela-Kerscher & F.J. Slack Oncomirs - microRNAs with a role in
cancer. Nat Rev Cancer 2006, 6(4):259-269, 2006.
[8] B Zhang, X Pan, GP Cobb, TA Anderson.. microRNAs as oncogenes and
tumor suppressors. Dev Biol. 302(1):1-12, 2007.
[9] P. Sethupathy, B. Corda and A.G Hatzigeorgiou., TarBase: A
comprehensive database of experimentally supported animal miRNA
targets, RNA, Vol. 12, pp.192-197, 2005.
[10] Shankavaram et al., Transcript and protein expression profiles of the
NCI-60 cancer cell panel: an integromic microarray study, Molecular
Cancer Therapeutics, Vol. 6, No. 3, pp.820-832, 2007
[11] Blower et. al., MiRNA expression profiles for the NCI-60 cancer cell
panel, Molecular Cancer Therapeutics, Vol. 6, No. 5, pp.1483-1491,
2007.
[12] Hsiang-Han.Chan and H. Sunny Sun, Identification of novel
tumor-associated gene (TAG) by bioinformatics analysis. Master Thesis,
Institute of Molecular Medicine, National Cheng Kung University, 2005.
[13] S Griffiths-Jones., Russell J. Grocock, Stijn van Dongen, Alex Bateman,
Anton J.Enright, miRBase: miRNA sequences, targets and gene
nomenclature, Nucleic Acids Research, Vol. 34, pp.140-144, 2006.
[14] Calin et al. Human microRNA genes are frequently located at fragile sites
and genomic regions involved in cancers. Proc Natl Acad Sci U S A,
101(9):2999-3004, 2004.
[15] Debacker Kim and R.Frank Kooy. Fragile sites and human disease.
Human Molecular Genetics, 16(2), R150-158, 2007.
[16] Kuan-Ting Lin, Chia-Hung Liu, Jen-Jie Chiou, Wen-Hsien Tseng,
Kuang-Lung Lin, Chun-Nan Hsu, Gene Name Service: No-Nonsense
Alias Resolution Service for Homo Sapiens Genes, Proceedings of the
2007 IEEE/WIC/ACM International Conferences on Web Intelligence
and Intelligent Agent Technology-Workshops, pp.185-188, 2007.
[17] A Cimmino et al.,. miR-15 and miR-16 induce apoptosis by targeting
BCL2. Proc Natl Acad Sci., 102(39):13944-9, 2005. Erratum in: Proc
Natl Acad Sci 14;103(7):2464, 2006..
[18] L Xia, D Zhang, R Du, Y Pan, L Zhao, S Sun, L Hong, J Liu, D Fan.
miR-15b and miR-16 modulate multidrug resistance by targeting BCL2 in
human gastric cancer cells. Int J Cancer. 123(2):372-9, 2008.
@article{"International Journal of Information, Control and Computer Sciences:52395", author = "Chien-Hung Huang and Chia-Wei Weng and Chang-Chih Chiang and Shih-Hua Wu and Chih-Hsien Huang and Ka-Lok Ng", title = "A study of Cancer-related MicroRNAs through Expression Data and Literature Search", abstract = "MicroRNAs (miRNAs) are a class of non-coding
RNAs that hybridize to mRNAs and induce either translation
repression or mRNA cleavage. Recently, it has been reported that
miRNAs could possibly play an important role in human diseases. By
integrating miRNA target genes, cancer genes, miRNA and mRNA
expression profiles information, a database is developed to link
miRNAs to cancer target genes. The database provides experimentally
verified human miRNA target genes information, including oncogenes
and tumor suppressor genes. In addition, fragile sites information for
miRNAs, and the strength of the correlation of miRNA and its target
mRNA expression level for nine tissue types are computed, which
serve as an indicator for suggesting miRNAs could play a role in
human cancer. The database is freely accessible at
http://ppi.bioinfo.asia.edu.tw/mirna_target/index.html.", keywords = "MicroRNA, miRNA expression profile, mRNAexpression profile, cancer genes, oncogene, tumor suppressor gene", volume = "3", number = "4", pages = "970-3", }