A novel framework for inferring condition-specific TF and miRNA co-regulation of protein-protein interactions.
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Jiuyong Li | T. Le | Lin Liu | Junpeng Zhang | Jianfeng He
[1] L. Dailey,et al. High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics. , 2015, Genomics.
[2] R. Gregory,et al. MicroRNA biogenesis pathways in cancer , 2015, Nature Reviews Cancer.
[3] Volkhard Helms,et al. TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks , 2015, Nucleic Acids Res..
[4] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[5] Julian Mintseris,et al. Transcription factor networks in Drosophila melanogaster. , 2014, Cell reports.
[6] Hsuan-Cheng Huang,et al. Mirin: identifying microRNA regulatory modules in protein-protein interaction networks , 2014, Bioinform..
[7] Ting Wang,et al. OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs , 2014, Bioinform..
[8] Lili Xiong,et al. Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues , 2014, Scientific Reports.
[9] D. Greenbaum,et al. Genome-Wide Survey , 2014 .
[10] Yi-Ping Phoebe Chen,et al. Computational developments in microRNA-regulated protein-protein interactions , 2014, BMC Systems Biology.
[11] Aihua Wang,et al. Exploring and exploiting the fundamental role of microRNAs in tumor pathogenesis , 2013, OncoTargets and therapy.
[12] Joshua M. Stuart,et al. The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.
[13] Jiuyong Li,et al. Inferring microRNA and transcription factor regulatory networks in heterogeneous data , 2013, BMC Bioinformatics.
[14] Hongjing Han,et al. miRCancer: a microRNA-cancer association database constructed by text mining on literature , 2013, Bioinform..
[15] Tom Michoel,et al. Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t-tests , 2012, Bioinform..
[16] Holger Fröhlich,et al. Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data , 2012, Bioinform..
[17] Yen-Jen Oyang,et al. Crosstalk between transcription factors and microRNAs in human protein interaction network , 2012, BMC Systems Biology.
[18] R. Sanz-Pamplona,et al. Tools for protein-protein interaction network analysis in cancer research , 2012, Clinical and Translational Oncology.
[19] Damian Roqueiro,et al. Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures , 2011, Proteome Science.
[20] Fabian J. Theis,et al. MicroRNAs coordinately regulate protein complexes , 2011, BMC Systems Biology.
[21] Hei-Chia Wang,et al. Inference of transcriptional regulatory network by bootstrapping patterns , 2011, Bioinform..
[22] David J. Arenillas,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 , 2011, BMC Bioinformatics.
[23] W. Filipowicz,et al. The widespread regulation of microRNA biogenesis, function and decay , 2010, Nature Reviews Genetics.
[24] Ivan Merelli,et al. A multilevel data integration resource for breast cancer study , 2010, BMC Systems Biology.
[25] Robi Tacutu,et al. MicroRNA-regulated protein-protein interaction networks: how could they help in searching for pro-longevity targets? , 2010, Rejuvenation research.
[26] Fabian J Theis,et al. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes , 2010, Genome Biology.
[27] Shuli Kang,et al. Clustered microRNAs' coordination in regulating protein-protein interaction network , 2009, BMC Systems Biology.
[28] Juan M. Vaquerizas,et al. A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.
[29] D. Bartel. MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.
[30] Yadong Wang,et al. miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..
[31] Q. Cui,et al. An Analysis of Human MicroRNA and Disease Associations , 2008, PloS one.
[32] Chun-Wei Hsu,et al. Characterization of microRNA‐regulated protein‐protein interaction network , 2008, Proteomics.
[33] Fidel Ramírez,et al. Computing topological parameters of biological networks , 2008, Bioinform..
[34] Simo V. Zhang,et al. A map of human cancer signaling , 2007, Molecular systems biology.
[35] Wen-Hsiung Li,et al. MicroRNA regulation of human protein protein interaction network. , 2007, RNA.
[36] Phillip D Zamore,et al. Beginning to understand microRNA function , 2007, Cell Research.
[37] Yitzhak Pilpel,et al. Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network , 2007, PLoS Comput. Biol..
[38] Gary D Bader,et al. NetMatch: a Cytoscape plugin for searching biological networks , 2007, Bioinform..
[39] Edwin Wang,et al. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. , 2006, Biochemical and biophysical research communications.
[40] Sarka Pospisilova,et al. MicroRNA biogenesis, functionality and cancer relevance. , 2006, Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia.
[41] M. Gerstein,et al. Genomic analysis of the hierarchical structure of regulatory networks , 2006, Proceedings of the National Academy of Sciences.
[42] Q. Cui,et al. Principles of microRNA regulation of a human cellular signaling network , 2006, Molecular systems biology.
[43] Wen-Shyen E. Chen,et al. CRSD: a comprehensive web server for composite regulatory signature discovery , 2006, Nucleic Acids Res..
[44] N. Rajewsky. microRNA target predictions in animals , 2006, Nature Genetics.
[45] K. S. Deshpande,et al. Human protein reference database—2006 update , 2005, Nucleic Acids Res..
[46] C. Burge,et al. Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.
[47] Alan F. Scott,et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..
[48] Zhiping Weng,et al. PromoSer: improvements to the algorithm, visualization and accessibility , 2004, Nucleic Acids Res..
[49] K. Becker,et al. The Genetic Association Database , 2004, Nature Genetics.
[50] T. Hubbard,et al. A census of human cancer genes , 2004, Nature Reviews Cancer.
[51] Z. Oltvai,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[52] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[53] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[54] E. Nimwegen. Scaling Laws in the Functional Content of Genomes , 2003, physics/0307001.
[55] V. Ambros. MicroRNA Pathways in Flies and Worms Growth, Death, Fat, Stress, and Timing , 2003, Cell.
[56] S. Shen-Orr,et al. Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.
[57] V. Ambros. microRNAs Tiny Regulators with Great Potential , 2001, Cell.
[58] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[59] David L. Steffen,et al. The Breast Cancer Gene Database: a collaborative information resource , 1999, Oncogene.
[60] Michael R. Green,et al. Transcription Factors and Human Disease , 1999, Nature Medicine.
[61] Shigeru Takasaki. Roles of microRNAs in cancers and development. , 2015, Methods in molecular biology.
[62] Hong-Mei Zhang,et al. Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases , 2015, Briefings Bioinform..
[63] S. Barik,et al. MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions. , 2011, Molecular and cellular pharmacology.
[64] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[65] Liu Cc,et al. (Nucleic Acids Res., 34:W571-W577)CRSD: a comprehensive web server for composite regulatory signature discovery , 2006 .
[66] E. Wingender,et al. TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..
[67] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[68] P. Atadja,et al. Regulation of transcription factor activity during cellular aging. , 1996, Biochemistry and cell biology = Biochimie et biologie cellulaire.
[69] T. Pawson,et al. Signal transduction--a conserved pathway from the membrane to the nucleus. , 1993, Developmental genetics.
[70] C. Lobe,et al. Transcription factors and mammalian development. , 1992, Current topics in developmental biology.