Epigenetically driven network cooperativity: meta-analysis in multi-drug resistant osteosarcoma

[1]  Nazar Zaki,et al.  Ensemble inference by integrative cancer networks , 2014, Front. Genet..

[2]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[3]  Mason A. Porter,et al.  Multilayer Analysis and Visualization of Networks , 2014, J. Complex Networks.

[4]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[5]  Christian von Mering,et al.  A sentinel protein assay for simultaneously quantifying cellular processes , 2014, Nature Methods.

[6]  Tamás Korcsmáros,et al.  Adaptation and learning of molecular networks as a description of cancer development at the systems-level: potential use in anti-cancer therapies. , 2013, Seminars in cancer biology.

[7]  J. Westendorf,et al.  Wnt signaling in osteoblasts and bone diseases. , 2004, Gene.

[8]  P. Sorger,et al.  Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks , 2012, Cell.

[9]  Stefan Wuchty,et al.  Controllability in protein interaction networks , 2014, Proceedings of the National Academy of Sciences.

[10]  M. Montenegro,et al.  Targeting the epigenetic machinery of cancer cells , 2014, Oncogene.

[11]  D. Pe’er,et al.  Principles and Strategies for Developing Network Models in Cancer , 2011, Cell.

[12]  R. Meehan,et al.  Non-canonical functions of the DNA methylome in gene regulation. , 2013, The Biochemical journal.

[13]  D. Patel,et al.  Readout of epigenetic modifications. , 2013, Annual review of biochemistry.

[14]  Junfeng Xia,et al.  Do cancer proteins really interact strongly in the human protein-protein interaction network? , 2011, Comput. Biol. Chem..

[15]  Thomas M. Cover,et al.  Elements of Information Theory: Cover/Elements of Information Theory, Second Edition , 2005 .

[16]  L. Stein,et al.  A human functional protein interaction network and its application to cancer data analysis , 2010, Genome Biology.

[17]  Jaewoo Kang,et al.  Automatic Context-Specific Subnetwork Discovery from Large Interaction Networks , 2014, PloS one.

[18]  H. McMurray,et al.  Gene signature critical to cancer phenotype as a paradigm for anticancer drug discovery , 2013, Oncogene.

[19]  Stefano Caserta,et al.  T‐cell receptor proximal signaling via the Src‐family kinases, Lck and Fyn, influences T‐cell activation, differentiation, and tolerance , 2009, Immunological reviews.

[20]  Eberhard Korsching,et al.  How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation , 2013, PLoS Comput. Biol..

[21]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[22]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[23]  Ali Masoudi-Nejad,et al.  Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes , 2013, PloS one.

[24]  F. Müller,et al.  Few inputs can reprogram biological networks , 2011, Nature.

[25]  E. Capobianco,et al.  Integrative analysis of cancer imaging readouts by networks , 2014, Molecular oncology.

[26]  C. Deng,et al.  TGF-β and BMP Signaling in Osteoblast Differentiation and Bone Formation , 2012, International journal of biological sciences.

[27]  Wan-chun Wang,et al.  Epigenetic changes in osteosarcoma. , 2011, Bulletin du cancer.

[28]  Gary D. Bader,et al.  GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop , 2010, Bioinform..

[29]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[30]  Ian M. Donaldson,et al.  iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database , 2011, BMC Bioinformatics.

[31]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[32]  Eivind Hovig,et al.  Integrative Analysis Reveals Relationships of Genetic and Epigenetic Alterations in Osteosarcoma , 2012, PloS one.

[33]  Jörg Schultz,et al.  Protein Interaction Networks—More Than Mere Modules , 2008, PLoS Comput. Biol..

[34]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[35]  Peter A. Jones,et al.  Epigenetics in cancer. , 2010, Carcinogenesis.

[36]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[37]  David M. Thomas,et al.  Translational biology of osteosarcoma , 2014, Nature Reviews Cancer.

[38]  Natapol Pornputtapong,et al.  A dedicated database system for handling multi-level data in systems biology , 2014, Source Code for Biology and Medicine.

[39]  David M. Thomas,et al.  Epigenetic modifications in osteogenic differentiation and transformation , 2006, Journal of cellular biochemistry.

[40]  Luciano da Fontoura Costa,et al.  Rich-club phenomenon across complex network hierarchies , 2007 .

[41]  Xiaoli Li,et al.  Inferring Gene-Phenotype Associations via Global Protein Complex Network Propagation , 2011, PloS one.

[42]  Gary D. Bader,et al.  The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function , 2010, Nucleic Acids Res..

[43]  B. Andrews,et al.  Neighboring-gene effect: a genetic uncertainty principle , 2012, Nature Methods.

[44]  A. Cleton-Jansen,et al.  Inactive Wnt/β‐catenin pathway in conventional high‐grade osteosarcoma , 2010, The Journal of pathology.

[45]  Pietro Liò,et al.  Comorbidity networks: beyond disease correlations , 2015, J. Complex Networks.

[46]  C. Cinti,et al.  Separate and Combined Effects of DNMT and HDAC Inhibitors in Treating Human Multi-Drug Resistant Osteosarcoma HosDXR150 Cell Line , 2014, PloS one.

[47]  A. Bonato,et al.  Dominating Biological Networks , 2011, PloS one.

[48]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[49]  Igor Jurisica,et al.  In silico prediction of physical protein interactions and characterization of interactome orphans , 2014, Nature Methods.

[50]  Gianluca Bontempi,et al.  minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information , 2008, BMC Bioinformatics.

[51]  I. Androulakis,et al.  Analysis of regulatory and interaction networks from clusters of co-expressed genes , 2013 .

[52]  Michel Dumontier,et al.  Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics , 2012, Bioinform..

[53]  Alessandro Vespignani,et al.  Detecting rich-club ordering in complex networks , 2006, physics/0602134.

[54]  M. Esteller,et al.  Cancer epigenetics reaches mainstream oncology , 2011, Nature Medicine.

[55]  J. Herman,et al.  DNA hypermethylation in tumorigenesis: epigenetics joins genetics. , 2000, Trends in genetics : TIG.

[56]  E. Fraenkel,et al.  Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks , 2009, Science Signaling.

[57]  Albert-László Barabási,et al.  Controllability of complex networks , 2011, Nature.

[58]  Anne-Marie Cleton-Jansen,et al.  Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data , 2012, Genes, chromosomes & cancer.

[59]  Riet De Smet,et al.  Advantages and limitations of current network inference methods , 2010, Nature Reviews Microbiology.

[60]  Rune Linding,et al.  Navigating cancer network attractors for tumor-specific therapy , 2012, Nature Biotechnology.