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BioMed Research International
Volume 2014 (2014), Article ID 623078, 8 pages
Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles
1Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
2Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112, Taiwan
3Mackay Medicine, Nursing and Management College, Taipei 112, Taiwan
4Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan
5Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan
6Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
7Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
8Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
9Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
Received 11 March 2014; Revised 2 May 2014; Accepted 18 May 2014; Published 9 June 2014
Academic Editor: Tzong-Yi Lee
Copyright © 2014 Chia-Hung Chien et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- S. M. Khoshnaw, A. R. Green, D. G. Powe, and I. O. Ellis, “MicroRNA involvement in the pathogenesis and management of breast cancer,” Journal of Clinical Pathology, vol. 62, no. 5, pp. 422–428, 2009.
- R. Schickel, B. Boyerinas, S.-M. Park, and M. E. Peter, “MicroRNAs: key players in the immune system, differentiation, tumorigenesis and cell death,” Oncogene, vol. 27, no. 45, pp. 5959–5974, 2008.
- H. K. Saini, S. Griffiths-Jones, and A. J. Enright, “Genomic analysis of human microRNA transcripts,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 45, pp. 17719–17724, 2007.
- H. K. Saini, A. J. Enright, and S. Griffiths-Jones, “Annotation of mammalian primary microRNAs,” BMC Genomics, vol. 9, article 564, 2008.
- J. Qian, Z. Zhang, J. Liang et al., “The full-length transcripts and promoter analysis of intergenic microRNAs in Drosophila melanogaster,” Genomics, vol. 97, no. 5, pp. 294–303, 2011.
- A. Barski, R. Jothi, S. Cuddapah et al., “Chromatin poises miRNA- and protein-coding genes for expression,” Genome Research, vol. 19, no. 10, pp. 1742–1751, 2009.
- C.-H. Chien, Y.-M. Sun, W.-C. Chang et al., “Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data,” Nucleic Acids Research, vol. 39, no. 21, pp. 9345–9356, 2011.
- M. Bhattacharyya, L. Feuerbach, T. Bhadra, T. Lengauer, and S. Bandyopadhyay, “MicroRNA transcription start site prediction with multi-objective feature selection,” Statistical Applications in Genetics and Molecular Biology, vol. 11, no. 1, article 6, 2012.
- Y. Saito, H. Suzuki, T. Taya et al., “Development of a novel microRNA promoter microarray for ChIP-on-chip assay to identify epigenetically regulated microRNAs,” Biochemical and Biophysical Research Communications, vol. 426, no. 1, pp. 33–37, 2012.
- J. Wang, M. Lu, C. Qiu, and Q. Cui, “TransmiR: a transcription factor microRNA regulation database,” Nucleic Acids Research, vol. 38, supplement 1, pp. D119–D122, 2009.
- R. Shalgi, D. Lieber, M. Oren, and Y. Pilpel, “Global and local architecture of the mammalian microRNA-transcription factor regulatory network,” PLoS Computational Biology, vol. 3, no. 7, article e131, 2007.
- C.-Y. Chen, S.-T. Chen, C.-S. Fuh, H.-F. Juan, and H.-C. Huang, “Coregulation of transcription factors and microRNAs in human transcriptional regulatory network,” BMC Bioinformatics, vol. 12, supplement 1, article S41, 2011.
- A. Re, D. Core, D. Taverna, and M. Caselle, “Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human,” Molecular BioSystems, vol. 5, no. 8, pp. 854–867, 2009.
- O. Friard, A. Re, D. Taverna, M. de Bortoli, and D. Corá, “CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse,” BMC Bioinformatics, vol. 11, article 435, 2010.
- A. le Bechec, E. Portales-Casamar, G. Vetter et al., “MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model,” BMC Bioinformatics, vol. 12, article 67, 2011.
- H. Naeem, R. Kuffner, and R. Zimmer, “MIRTFnet: analysis of miRNA regulated transcription factors,” PLoS ONE, vol. 6, no. 8, article e22519, 2011.
- X. Li, W. Jiang, W. Li et al., “Dissection of human miRNA regulatory influence to subpathway,” Briefings in Bioinformatics, vol. 13, no. 2, pp. 175–186, 2012.
- M. Beckstette, R. Homann, R. Giegerich, and S. Kurtz, “Fast index based algorithms and software for matching position specific scoring matrices,” BMC Bioinformatics, vol. 7, article 389, 2006.
- M. C. Frith, J. L. Spouge, U. Hansen, and Z. Weng, “Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences,” Nucleic Acids Research, vol. 30, no. 14, pp. 3214–3224, 2002.
- S. Rahmann, T. Muller, and M. Vingron, “On the power of profiles for transcription factor binding site detection,” Statistical Applications in Genetics and Molecular Biology, vol. 2, article 7, 2003.
- Y. M. Oh, J. K. Kim, S. Choi, and J.-Y. Yoo, “Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices,” Nucleic Acids Research, vol. 40, no. 5, article e38, 2012.
- V. Matys, E. Fricke, R. Geffers et al., “TRANSFAC: transcriptional regulation, from patterns to profiles,” Nucleic Acids Research, vol. 31, no. 1, pp. 374–378, 2003.
- E. Portales-Casamar, S. Thongjuea, A. T. Kwon et al., “JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles,” Nucleic Acids Research, vol. 38, supplement 1, pp. D105–D110, 2010.
- S. Aerts, G. Thijs, B. Coessens, M. Staes, Y. Moreau, and B. de Moor, “Toucan: deciphering the cis-regulatory logic of coregulated genes,” Nucleic Acids Research, vol. 31, no. 6, pp. 1753–1764, 2003.
- T. T. Marstrand, J. Frellsen, I. Moltke et al., “Asap: a framework for over-representation statistics for transcription factor binding sites,” PLoS ONE, vol. 3, no. 2, article e1623, 2008.
- F. Zambelli, G. Pesole, and G. Pavesi, “Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes,” Nucleic Acids Research, vol. 37, supplement 2, pp. W247–W252, 2009.
- S. J. H. Sui, J. R. Mortimer, D. J. Arenillas et al., “oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes,” Nucleic Acids Research, vol. 33, no. 10, pp. 3154–3164, 2005.
- A. Kozomara and S. Griffiths-Jones, “miRBase: integrating microRNA annotation and deep-sequencing data,” Nucleic Acids Research, vol. 39, supplement 1, pp. D152–D157, 2011.
- T. R. Dreszer, D. Karolchik, A. S. Zweig et al., “The UCSC Genome Browser database: extensions and updates 2011,” Nucleic Acids Research, vol. 40, supplement 1, pp. D918–D923, 2012.
- A. I. Su, T. Wiltshire, S. Batalov et al., “A gene atlas of the mouse and human protein-encoding transcriptomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 16, pp. 6062–6067, 2004.
- T. Barrett, D. B. Troup, S. E. Wilhite et al., “NCBI GEO: mining tens of millions of expression profiles—database and tools update,” Nucleic Acids Research, vol. 35, supplement 1, pp. D760–D765, 2007.
- Y. Liang, D. Ridzon, L. Wong, and C. Chen, “Characterization of microRNA expression profiles in normal human tissues,” BMC Genomics, vol. 8, article 166, 2007.
- C. Cheadle, M. P. Vawter, W. J. Freed, and K. G. Becker, “Analysis of microarray data using Z score transformation,” The Journal of Molecular Diagnostics, vol. 5, no. 2, pp. 73–81, 2003.
- P. Flicek, I. Ahmed, M. R. Amode, et al., “Ensembl 2013,” Nucleic Acids Research, vol. 41, no. 1, pp. D48–D55, 2013.
- A. E. Kel, E. Gossling, I. Reuter, E. Cheremushkin, O. V. Kel-Margoulis, and E. Wingender, “MATCH: a tool for searching transcription factor binding sites in DNA sequences,” Nucleic Acids Research, vol. 31, no. 13, pp. 3576–3579, 2003.
- W.-C. Tsai, S.-D. Hsu, C.-S. Hsu et al., “MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis,” The Journal of Clinical Investigation, vol. 122, no. 8, pp. 2884–2897, 2012.
- Z. Y. Li, Y. Xi, W. N. Zhu, et al., “Positive regulation of hepatic miR-122 expression by HNF4α,” Journal of Hepatology, vol. 55, no. 3, pp. 602–611, 2011.
- C. Coulouarn, V. M. Factor, J. B. Andersen, M. E. Durkin, and S. S. Thorgeirsson, “Loss of miR-122 expression in liver cancer correlates with suppression of the hepatic phenotype and gain of metastatic properties,” Oncogene, vol. 28, no. 40, pp. 3526–3536, 2009.
- H. de The, A. Marchio, P. Tiollais, and A. Dejean, “A novel steroid thyroid hormone receptor-related gene inappropriately expressed in human hepatocellular carcinoma,” Nature, vol. 330, no. 6149, pp. 667–670, 1987.
- Y. Wang, H. C. Toh, P. Chow et al., “MicroRNA-224 is up-regulated in hepatocellular carcinoma through epigenetic mechanisms,” The FASEB Journal, vol. 26, no. 7, pp. 3032–3041, 2012.
- J. Qin, M. J. Li, P. Wang, M. Q. Zhang, and J. Wang, “ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor,” Nucleic Acids Research, vol. 39, supplement 2, pp. W430–W436, 2011.
- M. Hu, J. Yu, J. M. Taylor, A. M. Chinnaiyan, and Z. S. Qin, “On the detection and refinement of transcription factor binding sites using ChIP-Seq data,” Nucleic Acids Research, vol. 38, no. 7, pp. 2154–2167, 2010.
- T. Handstad, M. B. Rye, F. Drablos, and P. Sætrom, “A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites,” PLoS ONE, vol. 6, no. 4, article e18430, 2011.