Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma
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Zhongming Zhao | Jingchun Sun | Xue Gong | Benjamin Purow | Zhongming Zhao | Jingchun Sun | B. Purow | Xue Gong | Zhongming Zhao
[1] Zhongming Zhao,et al. A comparative study of cancer proteins in the human protein-protein interaction network , 2010, BMC Genomics.
[2] Xi Chen,et al. An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies , 2011, Bioinform..
[3] An-Yuan Guo,et al. A Novel microRNA and transcription factor mediated regulatory network in schizophrenia , 2010, BMC Systems Biology.
[4] N. Rajewsky,et al. Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.
[5] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[6] E. Holland,et al. Glioblastoma multiforme: the terminator. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[7] Alexander E. Kel,et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes , 2005, Nucleic Acids Res..
[8] Jana Novakova,et al. MicroRNA involvement in glioblastoma pathogenesis. , 2009, Biochemical and biophysical research communications.
[9] Jennifer A Fulcher,et al. Phagocytes, Granulocytes, and Myelopoiesis , 2022 .
[10] Lynn Doucette-Stamm,et al. A C . elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity , 2008 .
[11] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[12] Mitchel S Berger,et al. Contribution of Notch signaling activation to human glioblastoma multiforme. , 2007, Journal of neurosurgery.
[13] Torbjörn E. M. Nordling,et al. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma , 2011, Molecular systems biology.
[14] S. Gabriel,et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.
[15] Francesco Tomasello,et al. miR-21 and 221 upregulation and miR-181b downregulation in human grade II–IV astrocytic tumors , 2009, Journal of Neuro-Oncology.
[16] Alexander E. Kel,et al. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..
[17] Anton J. Enright,et al. Detection of functional modules from protein interaction networks , 2003, Proteins.
[18] Adam A. Margolin,et al. Reverse engineering cellular networks , 2006, Nature Protocols.
[19] Yadong Wang,et al. miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..
[20] Alexander R. Pico,et al. Variants in the CDKN2B and RTEL1 regions are associated with high grade glioma susceptibility , 2009, Nature Genetics.
[21] Yunqing Li,et al. MicroRNA-34a inhibits glioblastoma growth by targeting multiple oncogenes. , 2009, Cancer research.
[22] Dianne P. O'Leary,et al. Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality , 2008, PLoS Comput. Biol..
[23] C. Burge,et al. Prediction of Mammalian MicroRNA Targets , 2003, Cell.
[24] Sharmila Shankar,et al. Targeting Epigenetic Regulation of miR-34a for Treatment of Pancreatic Cancer by Inhibition of Pancreatic Cancer Stem Cells , 2011, PloS one.
[25] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[26] E. Davidson. The Regulatory Genome: Gene Regulatory Networks In Development And Evolution , 2006 .
[27] A. van Oudenaarden,et al. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. , 2007, Molecular cell.
[28] O. Hobert. Gene Regulation by Transcription Factors and MicroRNAs , 2008, Science.
[29] Yun Xiao,et al. MiRNA–miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features , 2010, Nucleic acids research.
[30] Chris Wiggins,et al. ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.
[31] Benjamin Purow,et al. Advances in the genetics of glioblastoma: are we reaching critical mass? , 2009, Nature Reviews Neurology.
[32] Qing-Rong Chen,et al. Systematic proteome analysis identifies transcription factor YY1 as a direct target of miR-34a. , 2011, Journal of proteome research.
[33] Claudia Petritsch,et al. miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells , 2008 .
[34] Yuri Kotliarov,et al. Prediction of Associations between microRNAs and Gene Expression in Glioma Biology , 2011, PloS one.
[35] Melissa Bondy,et al. Genome-wide association study identifies five susceptibility loci for glioma , 2009, Nature Genetics.
[36] Yong Jin Choi,et al. miR-34 miRNAs provide a barrier for somatic cell reprogramming , 2011, Nature Cell Biology.
[37] Kai-Fai Lee,et al. MicroRNA-34a suppresses invasion through downregulation of Notch1 and Jagged1 in cervical carcinoma and choriocarcinoma cells. , 2010, Carcinogenesis.
[38] Trey Ideker,et al. Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..
[39] S. Ivy,et al. Targeting cancer stem cells by inhibiting Wnt, Notch, and Hedgehog pathways , 2011, Nature Reviews Clinical Oncology.
[40] Sharon J. Diskin,et al. A Functional Screen Identifies miR-34a as a Candidate Neuroblastoma Tumor Suppressor Gene , 2008, Molecular Cancer Research.
[41] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[42] Joshua M. Korn,et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.
[43] C. Croce,et al. A microRNA expression signature of human solid tumors defines cancer gene targets , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[44] Fei Chen,et al. Effect of microRNA‐34a in cell cycle, differentiation, and apoptosis: A review , 2012, Journal of biochemical and molecular toxicology.
[45] Ana Kozomara,et al. miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..
[46] F. Slack,et al. Oncomirs — microRNAs with a role in cancer , 2006, Nature Reviews Cancer.
[47] Sujaya Srinivasan,et al. A Ten-microRNA Expression Signature Predicts Survival in Glioblastoma , 2011, PloS one.
[48] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[49] Doron Betel,et al. The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..
[50] Alice Shapiro,et al. MicroRNA-21 targets a network of key tumor-suppressive pathways in glioblastoma cells. , 2008, Cancer research.
[51] T. Wurdinger,et al. MicroRNA 21 Promotes Glioma Invasion by Targeting Matrix Metalloproteinase Regulators , 2008, Molecular and Cellular Biology.
[52] W. Cho. OncomiRs: the discovery and progress of microRNAs in cancers , 2007, Molecular Cancer.
[53] Yibo Wu,et al. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products , 2010, Bioinform..
[54] Alan F. Scott,et al. McKusick's Online Mendelian Inheritance in Man (OMIM®) , 2008, Nucleic Acids Res..
[55] C. Sander,et al. Automated Network Analysis Identifies Core Pathways in Glioblastoma , 2010, PloS one.
[56] Dustin E. Schones,et al. Chromatin poises miRNA- and protein-coding genes for expression. , 2009, Genome research.
[57] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[58] Yitzhak Pilpel,et al. Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network , 2007, PLoS Comput. Biol..
[59] E. Wingender,et al. MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.
[60] J Khan,et al. The MYCN oncogene is a direct target of miR-34a , 2008, Oncogene.
[61] Yanghua Xiao,et al. Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma , 2010, BMC Systems Biology.
[62] D. Goldberg,et al. Assessing experimentally derived interactions in a small world , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[63] N. Campbell. Genetic association database , 2004, Nature Reviews Genetics.
[64] S. L. Wong,et al. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network , 2005, Journal of biology.
[65] Mingming Jia,et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer , 2010, Nucleic Acids Res..
[66] Giuseppe Basso,et al. MiR-34a Targeting of Notch Ligand Delta-Like 1 Impairs CD15+/CD133+ Tumor-Propagating Cells and Supports Neural Differentiation in Medulloblastoma , 2011, PloS one.
[67] Shipra Agrawal,et al. Cancer esearch rated Systems and Technologies blastoma-Specific Protein Interaction Network Identifies A and CSK 21 as Connecting Molecules between R l Cycle – Associated Genes , 2010 .
[68] M. Gerstein,et al. Genomic analysis of essentiality within protein networks. , 2004, Trends in genetics : TIG.
[69] S. Shen-Orr,et al. Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.
[70] Bing Zhang,et al. WebGestalt: an integrated system for exploring gene sets in various biological contexts , 2005, Nucleic Acids Res..
[71] Yunqing Li,et al. microRNA-34a is tumor suppressive in brain tumors and glioma stem cells , 2010, Cell cycle.
[72] Q. Su,et al. Expression of Notch-1 and its ligands, Delta-like-1 and Jagged-1, is critical for glioma cell survival and proliferation. , 2005, Cancer research.
[73] D. Bartel,et al. The impact of microRNAs on protein output , 2008, Nature.
[74] B. Sosa-Pineda,et al. The gene Pax4 is an essential regulator of pancreatic beta-cell development. , 2004, Molecules and cells.
[75] Tae-Min Kim,et al. A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. , 2011, Cancer research.
[76] F. Ferrari,et al. Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation , 2008, Nucleic acids research.
[77] K. Kosik,et al. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. , 2005, Cancer research.
[78] Gabriele Schackert,et al. Long-term survival with glioblastoma multiforme. , 2007, Brain : a journal of neurology.
[79] Robert W. Zeller,et al. miR-124 function during Ciona intestinalis neuronal development includes extensive interaction with the Notch signaling pathway , 2011, Development.
[80] Q. Cui,et al. An Analysis of Human MicroRNA and Disease Associations , 2008, PloS one.
[81] J. Parker,et al. A feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle. , 2009, Cancer research.
[82] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[83] D. Busam,et al. An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.
[84] K. Gunsalus,et al. Combinatorial microRNA target predictions , 2005, Nature Genetics.
[85] Varda Rotter,et al. Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate , 2009, Aging.
[86] L. Lim,et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.
[87] Illés J. Farkas,et al. CFinder: locating cliques and overlapping modules in biological networks , 2006, Bioinform..
[88] Fabian J Theis,et al. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes , 2010, Genome Biology.
[89] Bing Zhang,et al. Network-assisted protein identification and data interpretation in shotgun proteomics , 2009, Molecular systems biology.
[90] Benjamin Purow,et al. The elephant in the room: do microRNA-based therapies have a realistic chance of succeeding for brain tumors such as glioblastoma? , 2011, Journal of Neuro-Oncology.