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Volumn 43, Issue W1, 2015, Pages W283-W288

TFmiR: A web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 155; TRANSCRIPTION FACTOR;

EID: 84979851759     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv418     Document Type: Article
Times cited : (41)

References (50)
  • 1
    • 41349096445 scopus 로고    scopus 로고
    • Gene regulation by transcription factors and micro RNAs
    • Hobert, O. (2008) Gene regulation by transcription factors and micro RNAs. Science, 319, 1785-1786.
    • (2008) Science , vol.319 , pp. 1785-1786
    • Hobert, O.1
  • 2
    • 33645294070 scopus 로고    scopus 로고
    • Oncomirs - Micro RNAs with a role in cancer
    • Esquela-Kerscher, A. and Slack, F.J. (2006) Oncomirs - micro RNAs with a role in cancer. Nat. Rev. Cancer, 6, 259-269.
    • (2006) Nat. Rev. Cancer , vol.6 , pp. 259-269
    • Esquela-Kerscher, A.1    Slack, F.J.2
  • 3
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of cancer: The next generation
    • Hanahan, D. and Weinberg, R.A. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674.
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 4
    • 84883331699 scopus 로고    scopus 로고
    • How micro RNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation
    • Poos, K., Smida, J., Nathrath, M., Maugg, D., Baumhoer, D. and Korsching, E. (2013) How micro RNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PLoS Comput. Biol., 9, e1003210.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003210
    • Poos, K.1    Smida, J.2    Nathrath, M.3    Maugg, D.4    Baumhoer, D.5    Korsching, E.6
  • 5
    • 84866929613 scopus 로고    scopus 로고
    • Integrative analysis of gene and miRNA expression profiles with transcription factor miRNA feed-forward loops identifies regulators in human cancers
    • Yan, Z., Shah, P.K., Amin, S.B., Samur, M.K., Huang, N., Wang, X., Misra, V., Ji, H., Gabuzda, D. and Li, C. (2012) Integrative analysis of gene and miRNA expression profiles with transcription factor miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res., 40, e135.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e135
    • Yan, Z.1    Shah, P.K.2    Amin, S.B.3    Samur, M.K.4    Huang, N.5    Wang, X.6    Misra, V.7    Ji, H.8    Gabuzda, D.9    Li, C.10
  • 6
    • 84969130589 scopus 로고    scopus 로고
    • Integrative network based approach identifies key genetic elements in breast invasive carcinoma
    • Hamed, M., Spaniol, C., Zapp, A. and Helms, V. (2015) Integrative network based approach identifies key genetic elements in breast invasive carcinoma. BMC Genomics, 16(Suppl. 5), S2.
    • (2015) BMC Genomics , vol.16 , pp. S2
    • Hamed, M.1    Spaniol, C.2    Zapp, A.3    Helms, V.4
  • 10
    • 75549092303 scopus 로고    scopus 로고
    • Transmi R: A transcription factor-micro RNA regulation database
    • Wang, J., Lu, M., Qiu, C. and Cui, Q. (2010) Transmi R: a transcription factor-micro RNA regulation database. Nucleic Acids Res., 38, D119-D122.
    • (2010) Nucleic Acids Res. , vol.38 , pp. D119-D122
    • Wang, J.1    Lu, M.2    Qiu, C.3    Cui, Q.4
  • 12
    • 31044444975 scopus 로고    scopus 로고
    • Tar base: A comprehensive database of experimentally supported animal micro RNA targets
    • Sethupathy, P., Corda, B. and Hatzigeorgiou, A.G. (2006) Tar Base: a comprehensive database of experimentally supported animal micro RNA targets. RNA, 12, 192-197.
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 13
    • 58149186499 scopus 로고    scopus 로고
    • MiRecords: An integrated resource for micro RNA-target interactions
    • Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X. and Li, T. (2009) miRecords: an integrated resource for micro RNA-target interactions. Nucleic Acids Res., 37, D105-D110.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D105-D110
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5    Li, T.6
  • 14
    • 84880303015 scopus 로고    scopus 로고
    • Regulation of cardiac micro RNAs by cardiac micro RNAs
    • Matkovich, S., Hu, Y. and Dorn, G. (2013) Regulation of cardiac micro RNAs by cardiac micro RNAs. Circ. Res., 113, 62-71.
    • (2013) Circ. Res. , vol.113 , pp. 62-71
    • Matkovich, S.1    Hu, Y.2    Dorn, G.3
  • 15
    • 79956144613 scopus 로고    scopus 로고
    • Participation of micro RNAs in human interactome: Extraction of micro RNA-micro RNA regulations
    • Sengupta, D. and Bandyopadhyay, S. (2011) Participation of micro RNAs in human interactome: extraction of micro RNA-micro RNA regulations. Mol. Bio Syst. 7, 1966-1973.
    • (2011) Mol. Bio Syst. , vol.7 , pp. 1966-1973
    • Sengupta, D.1    Bandyopadhyay, S.2
  • 16
    • 77953939085 scopus 로고    scopus 로고
    • Micro RNA evolution in a human transcription factor and micro RNA regulatory network
    • Qiu, C., Wang, J., Yao, P., Wang, E. and Cui, Q. (2010) Micro RNA evolution in a human transcription factor and micro RNA regulatory network. BMC Syst. Biol., 4, 90.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 90
    • Qiu, C.1    Wang, J.2    Yao, P.3    Wang, E.4    Cui, Q.5
  • 17
    • 78651307694 scopus 로고    scopus 로고
    • Star base: A database for exploring micro RNA mRNA interaction maps from argonaute CLIP-seq and degradome-seq data
    • Yang, J.-H., Li, J.-H., Shao, P., Zhou, H., Chen, Y.-Q. and Qu, L.-H. (2011) star Base: a database for exploring micro RNA mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res., 39, D202-D209.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D202-D209
    • Yang, J.-H.1    Li, J.-H.2    Shao, P.3    Zhou, H.4    Chen, Y.-Q.5    Qu, L.-H.6
  • 18
    • 58249088751 scopus 로고    scopus 로고
    • Micro RNAs: Target recognition and regulatory functions
    • Bartel, D.P. (2009) Micro RNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 20
    • 33748587841 scopus 로고    scopus 로고
    • A pattern-based method for the identification of Micro RNA binding sites and their corresponding heteroduplexes
    • Miranda, K., Huynh, T., Tay, Y., Ang, Y.S., Tam, W.L., Thomson, A.M., Lim, B. and Rigoutsos, I. (2006) A pattern-based method for the identification of Micro RNA binding sites and their corresponding heteroduplexes. Cell, 126, 1203-1217.
    • (2006) Cell , vol.126 , pp. 1203-1217
    • Miranda, K.1    Huynh, T.2    Tay, Y.3    Ang, Y.S.4    Tam, W.L.5    Thomson, A.M.6    Lim, B.7    Rigoutsos, I.8
  • 21
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in micro RNA target recognition
    • Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007) The role of site accessibility in micro RNA target recognition. Nat. Genet., 39, 1278-1284.
    • (2007) Nat. Genet. , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 23
    • 54849408182 scopus 로고    scopus 로고
    • An analysis of human micro RNA and disease associations
    • Lu, M., Zhang, Q., Deng, M., Miao, J., Guo, Y., Gao, W. and Cui, Q. (2008) An analysis of human micro RNA and disease associations. PLoS ONE, 3, e3420.
    • (2008) PLoS ONE , vol.3 , pp. e3420
    • Lu, M.1    Zhang, Q.2    Deng, M.3    Miao, J.4    Guo, Y.5    Gao, W.6    Cui, Q.7
  • 24
    • 78149236787 scopus 로고    scopus 로고
    • Dis Ge NET: A cytoscape plugin to visualize, integrate, search and analyze gene-disease networks
    • Bauer-Mehren, A., Rautschka, M., Sanz, F. and Furlong, L.I. (2010) Dis Ge NET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks. Bioinformatics (England), 26, 2924-2926.
    • (2010) Bioinformatics (England) , vol.26 , pp. 2924-2926
    • Bauer-Mehren, A.1    Rautschka, M.2    Sanz, F.3    Furlong, L.I.4
  • 25
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 27
    • 78149353689 scopus 로고    scopus 로고
    • A power aware minimum connected dominating set for wireless sensor networks
    • Rai, M., Verma, S. and Tapaswi, S. (2009) A power aware minimum connected dominating set for wireless sensor networks. J. Netw., 4, 511-519.
    • (2009) J. Netw. , vol.4 , pp. 511-519
    • Rai, M.1    Verma, S.2    Tapaswi, S.3
  • 28
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S.S., Milo, R., Mangan, S. and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet., 31, 64-68.
    • (2002) Nat. Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 30
    • 64249144494 scopus 로고    scopus 로고
    • A micro RNA imparts robustness against environmental fluctuation during development
    • Li, X., Cassidy, J.J., Reinke, C.A., Fischboeck, S. and Carthew, R.W. (2009) A micro RNA imparts robustness against environmental fluctuation during development. Cell, 137, 273-282.
    • (2009) Cell , vol.137 , pp. 273-282
    • Li, X.1    Cassidy, J.J.2    Reinke, C.A.3    Fischboeck, S.4    Carthew, R.W.5
  • 31
    • 84984686092 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B (Methodological), 57, 289-300.
    • (1995) J. R. Stat. Soc. B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 32
    • 77951942707 scopus 로고    scopus 로고
    • GOSem sim: An R package for measuring semantic similarity among GO terms and gene products
    • Yu, G., Li, F., Qin, Y., Bo, X., Wu, Y. and Wang, S. (2010) GOSem Sim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics, 26, 976-978.
    • (2010) Bioinformatics , vol.26 , pp. 976-978
    • Yu, G.1    Li, F.2    Qin, Y.3    Bo, X.4    Wu, Y.5    Wang, S.6
  • 33
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Koboldt, D.C., Fulton, R.S., McLellan, M.D. et al. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
    • (2012) Nature , vol.490 , pp. 61-70
    • Koboldt, D.C.1    Fulton, R.S.2    McLellan, M.D.3
  • 34
    • 27544491235 scopus 로고    scopus 로고
    • The enhanced tumor selectivity of an oncolytic vaccinia lacking the host range and antiapoptosis genes SPI-1 and SPI-2
    • Guo, Z., Naik, A., O'Malley, M., Popovic, P., Demarco, R., Hu, Y., Yin, X., Yang, S., Zeh, H. and Moss, B. (2005) The enhanced tumor selectivity of an oncolytic vaccinia lacking the host range and antiapoptosis genes SPI-1 and SPI-2. Cancer Res., 65, 9991-9998.
    • (2005) Cancer Res. , vol.65 , pp. 9991-9998
    • Guo, Z.1    Naik, A.2    O'Malley, M.3    Popovic, P.4    Demarco, R.5    Hu, Y.6    Yin, X.7    Yang, S.8    Zeh, H.9    Moss, B.10
  • 37
    • 84876566914 scopus 로고    scopus 로고
    • ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and micro RNA genes from ChIP-Seq data
    • Yang, J.-H., Li, J.-H., Jiang, S., Zhou, H. and Qu, L.-H. (2013) ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and micro RNA genes from ChIP-Seq data. Nucleic Acids Res., 41, D177-D187.
    • (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
  • 38
    • 77956520986 scopus 로고    scopus 로고
    • Circuits DB: A database of mixed micro RNA/transcription factor feed-forward regulatory circuits in human and mouse
    • Friard, O., Re, A., Taverna, D., De Bortoli, M. and Corá, D. (2010) Circuits DB: a database of mixed micro RNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinform., 11, 435.
    • (2010) BMC Bioinform. , vol.11 , pp. 435
    • Friard, O.1    Re, A.2    Taverna, D.3    De Bortoli, M.4    Corá, D.5
  • 39
    • 58149179989 scopus 로고    scopus 로고
    • MiR2 Disease: A manually curated database for micro RNA deregulation in human disease
    • Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G. and Liu, Y. (2009) miR2 Disease: a manually curated database for micro RNA deregulation in human disease. Nucleic Acids Res., 37, D98-D104.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D98-D104
    • Jiang, Q.1    Wang, Y.2    Hao, Y.3    Juan, L.4    Teng, M.5    Zhang, X.6    Li, M.7    Wang, G.8    Liu, Y.9
  • 40
    • 84902525655 scopus 로고    scopus 로고
    • CGRNB: A web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets
    • Xu, H., Yu, H., Tu, K., Shi, Q., Wei, C., Li, Y.-Y.Y. and Li, Y.-X.X. (2013) cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. BMC Syst. Biol., 7(Suppl. 2), S7.
    • (2013) BMC Syst. Biol. , vol.7 , pp. S7
    • Xu, H.1    Yu, H.2    Tu, K.3    Shi, Q.4    Wei, C.5    Li, Y.-Y.Y.6    Li, Y.-X.X.7
  • 41
    • 84877728814 scopus 로고    scopus 로고
    • Topological patterns in micro RNA gene regulatory network: Studies in colorectal and breast cancer
    • Sengupta, D. and Bandyopadhyay, S. (2013) Topological patterns in micro RNA gene regulatory network: studies in colorectal and breast cancer. Mol. Bio Syst., 9, 1360-1371.
    • (2013) Mol. Bio Syst. , vol.9 , pp. 1360-1371
    • Sengupta, D.1    Bandyopadhyay, S.2
  • 42
    • 84857204573 scopus 로고    scopus 로고
    • MiRTrail - A comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases
    • Laczny, C., Leidinger, P., Haas, J., Ludwig, N., Backes, C., Gerasch, A., Kaufmann, M., Vogel, B., Katus, H.A., Meder, B. et al. (2012) miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinform., 13, 36.
    • (2012) BMC Bioinform. , vol.13 , pp. 36
    • Laczny, C.1    Leidinger, P.2    Haas, J.3    Ludwig, N.4    Backes, C.5    Gerasch, A.6    Kaufmann, M.7    Vogel, B.8    Katus, H.A.9    Meder, B.10
  • 45
    • 62549134412 scopus 로고    scopus 로고
    • Micro RNA and colorectal cancer
    • Yang, L., Belaguli, N. and Berger, D. (2009) Micro RNA and colorectal cancer. W. J. Surg., 33, 638-646.
    • (2009) W. J. Surg. , vol.33 , pp. 638-646
    • Yang, L.1    Belaguli, N.2    Berger, D.3
  • 47
    • 84863643651 scopus 로고    scopus 로고
    • Key pathway miner: Detecting case-specific biological pathways using expression data
    • Alcaraz, N., Kck, H., Weile, J., Wipat, A. and Baumbach, J. (2011) Key Pathway Miner: detecting case-specific biological pathways using expression data. Internet Math., 7, 299-313.
    • (2011) Internet Math. , vol.7 , pp. 299-313
    • Alcaraz, N.1    Kck, H.2    Weile, J.3    Wipat, A.4    Baumbach, J.5
  • 48
    • 77953187312 scopus 로고    scopus 로고
    • GIGA: A simple, efficient algorithm for gene tree inference in the genomic age
    • Thomas, P. (2010) GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinform., 11, 312.
    • (2010) BMC Bioinform. , vol.11 , pp. 312
    • Thomas, P.1
  • 49
    • 79952389826 scopus 로고    scopus 로고
    • Algorithms for detecting significantly mutated pathways in cancer
    • Vandin, F., Upfal, E. and Raphael, B. (2011) Algorithms for detecting significantly mutated pathways in cancer. Comput. Biol., 18, 507-522.
    • (2011) Comput. Biol. , vol.18 , pp. 507-522
    • Vandin, F.1    Upfal, E.2    Raphael, B.3
  • 50
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker, T., Ozier, O., Schwikowski, B. and Siegel, A. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18, S233-S240.
    • (2002) Bioinformatics , vol.18 , pp. S233-S240
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.4


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