Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery

[1]  Michael R. Johnson,et al.  De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies. , 2014, American journal of human genetics.

[2]  Michael R. Johnson,et al.  Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery , 2016, Genome Biology.

[3]  Giovanni Coppola,et al.  A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program , 2016, Neuron.

[4]  T. Tomson,et al.  Valproic acid after five decades of use in epilepsy: time to reconsider the indications of a time-honoured drug , 2016, The Lancet Neurology.

[5]  Doug Speed,et al.  Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease , 2015, Nature Neuroscience.

[6]  A. Barabasi,et al.  Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets , 2015, Proceedings of the National Academy of Sciences.

[7]  S. C. Yenisetti,et al.  Neuropharmacological Properties of Withania somnifera - Indian Ginseng: An Overview on Experimental Evidence with Emphasis on Clinical Trials and Patents. , 2016, Recent patents on CNS drug discovery.

[8]  Staci A. Sorensen,et al.  Adult Mouse Cortical Cell Taxonomy Revealed by Single Cell Transcriptomics , 2016 .

[9]  Zhong Sheng Sun,et al.  Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database , 2016, Molecular Psychiatry.

[10]  F. Benfenati,et al.  Regulation of neural gene transcription by optogenetic inhibition of the RE1-silencing transcription factor , 2015, Proceedings of the National Academy of Sciences.

[11]  Allan R. Jones,et al.  Canonical Genetic Signatures of the Adult Human Brain , 2015, Nature Neuroscience.

[12]  M. Pirmohamed,et al.  Identifying the biological pathways underlying human focal epilepsy: from complexity to coherence to centrality. , 2015, Human molecular genetics.

[13]  Daniel H. Geschwind,et al.  Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders , 2015, Nature Reviews Genetics.

[14]  M. Krebs,et al.  Mutation Burden of Rare Variants in Schizophrenia Candidate Genes , 2015, PloS one.

[15]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[16]  Alejandro Sifrim,et al.  Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data , 2015, The Lancet.

[17]  S. Linnarsson,et al.  Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.

[18]  Slave Petrovski,et al.  Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus , 2015, Nature Communications.

[19]  P. Sullivan,et al.  CNV Concordance in 1,097 MZ Twin Pairs , 2015, Twin Research and Human Genetics.

[20]  Tomas W. Fitzgerald,et al.  Large-scale discovery of novel genetic causes of developmental disorders , 2014, Nature.

[21]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[22]  R. Fisher.  Redefining epilepsy. , 2015, Current opinion in neurology.

[23]  S. MacGregor,et al.  VEGAS2: Software for More Flexible Gene-Based Testing , 2014, Twin Research and Human Genetics.

[24]  Boris Yamrom,et al.  The contribution of de novo coding mutations to autism spectrum disorder , 2014, Nature.

[25]  H. Beck,et al.  Impaired Action Potential Initiation in GABAergic Interneurons Causes Hyperexcitable Networks in an Epileptic Mouse Model Carrying a Human NaV1.1 Mutation , 2014, The Journal of Neuroscience.

[26]  Christopher S. Poultney,et al.  Synaptic, transcriptional, and chromatin genes disrupted in autism , 2014, Nature.

[27]  Epilepsy Phenome,et al.  De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies. , 2014, American journal of human genetics.

[28]  Edouard Henrion,et al.  De Novo Mutations in Moderate or Severe Intellectual Disability , 2014, PLoS genetics.

[29]  A. Singleton,et al.  Genetic variability in the regulation of gene expression in ten regions of the human brain , 2014, Nature Neuroscience.

[30]  C. Bernard,et al.  The transcription factor NRSF contributes to epileptogenesis by selective repression of a subset of target genes , 2014, eLife.

[31]  Michael R. Johnson,et al.  Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies , 2014, The Lancet Neurology.

[32]  Michael R. Johnson,et al.  Describing the genetic architecture of epilepsy through heritability analysis , 2014, Brain : a journal of neurology.

[33]  Aidan Neligan,et al.  An unknown quantity—The worldwide prevalence of epilepsy , 2014, Epilepsia.

[34]  Søren Brunak,et al.  Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics , 2014, Nature Methods.

[35]  Samuel F. Berkovic,et al.  The hidden genetics of epilepsy—a clinically important new paradigm , 2014, Nature Reviews Neurology.

[36]  J. H. Cross,et al.  ILAE Official Report: A practical clinical definition of epilepsy , 2014, Epilepsia.

[37]  Mingfeng Li,et al.  Temporal Specification and Bilaterality of Human Neocortical Topographic Gene Expression , 2014, Neuron.

[38]  E. Banks,et al.  De novo mutations in schizophrenia implicate synaptic networks , 2014, Nature.

[39]  G. Tseng,et al.  Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders , 2014, Genes, brain, and behavior.

[40]  A. Pitkänen,et al.  Are alterations in transmitter receptor and ion channel expression responsible for epilepsies? , 2014, Advances in experimental medicine and biology.

[41]  Enrico Petretto,et al.  Leveraging gene co-expression networks to pinpoint the regulation of complex traits and disease, with a focus on cardiovascular traits. , 2014, Briefings in functional genomics.

[42]  A. Ramasamy,et al.  Widespread sex differences in gene expression and splicing in the adult human brain , 2013, Nature Communications.

[43]  S. Horvath,et al.  Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism , 2013, Cell.

[44]  Dieter Schmidt,et al.  New avenues for anti-epileptic drug discovery and development , 2013, Nature Reviews Drug Discovery.

[45]  L. Siever,et al.  Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network , 2013, Cell.

[46]  Jing Wang,et al.  WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 , 2013, Nucleic Acids Res..

[47]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[48]  M. Daly,et al.  Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis , 2013, The Lancet.

[49]  Peter Langfelder,et al.  When Is Hub Gene Selection Better than Standard Meta-Analysis? , 2013, PloS one.

[50]  Alexander E. Ivliev,et al.  Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach , 2013, PloS one.

[51]  David W. Evans,et al.  Developmental brain dysfunction: revival and expansion of old concepts based on new genetic evidence , 2013, The Lancet Neurology.

[52]  De novo mutations in epileptic encephalopathies , 2013 .

[53]  M. Mazzuferi,et al.  Rapid epileptogenesis in the mouse pilocarpine model: Video-EEG, pharmacokinetic and histopathological characterization , 2012, Experimental Neurology.

[54]  B. V. van Bon,et al.  Diagnostic exome sequencing in persons with severe intellectual disability. , 2012, The New England journal of medicine.

[55]  D. Horn,et al.  Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study , 2012, The Lancet.

[56]  S. Levy,et al.  De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia , 2012, Nature Genetics.

[57]  Allan R. Jones,et al.  An anatomically comprehensive atlas of the adult human brain transcriptome , 2012, Nature.

[58]  E. Eichler,et al.  Epi4K: Gene discovery in 4,000 genomes , 2012 .

[59]  Darcy Mcmullin.  Epi4K: Gene discovery in 4,000 genomes , 2012, Epilepsia.

[60]  Kenny Q. Ye,et al.  De Novo Gene Disruptions in Children on the Autistic Spectrum , 2012, Neuron.

[61]  Michael F. Walker,et al.  De novo mutations revealed by whole-exome sequencing are strongly associated with autism , 2012, Nature.

[62]  Bradley P. Coe,et al.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations , 2012, Nature.

[63]  R. Durbin,et al.  Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses , 2012, Nature Protocols.

[64]  Martin H. Schaefer,et al.  HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores , 2012, PloS one.

[65]  O. Steinlein.  Genetics of idiopathic epilepsies. , 2012, Handbook of clinical neurology.

[66]  J. Kleinman,et al.  Spatiotemporal transcriptome of the human brain , 2011, Nature.

[67]  C. Bernard,et al.  Neuron‐restrictive silencer factor‐mediated hyperpolarization‐activated cyclic nucleotide gated channelopathy in experimental temporal lobe epilepsy , 2011, Annals of neurology.

[68]  S. Lok,et al.  Increased exonic de novo mutation rate in individuals with schizophrenia , 2011, Nature Genetics.

[69]  I. Scheffer,et al.  Dravet syndrome as epileptic encephalopathy: evidence from long-term course and neuropathology , 2011, Brain : a journal of neurology.

[70]  S. Teichmann,et al.  RNA sequencing reveals two major classes of gene expression levels in metazoan cells , 2011, Molecular systems biology.

[71]  M. Daly,et al.  Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology , 2011, PLoS genetics.

[72]  Rui Luo,et al.  Is My Network Module Preserved and Reproducible? , 2011, PLoS Comput. Biol..

[73]  K. Yamakawa,et al.  Scn1a mice exhibit hyperactivity, autism-like behavioral deficits and learning impairments , 2010, Neuroscience Research.

[74]  Ian M. Donaldson,et al.  iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence , 2010, Database J. Biol. Databases Curation.

[75]  Rainer Breitling,et al.  DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules , 2010, BMC Bioinformatics.

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

[77]  Sangsoo Kim,et al.  GSA-SNP: a general approach for gene set analysis of polymorphisms , 2010, Nucleic Acids Res..

[78]  J. H. Cross,et al.  Revised terminology and concepts for organization of seizures and epilepsies: Report of the ILAE Commission on Classification and Terminology, 2005–2009 , 2010, Epilepsia.

[79]  Christian Bottomley,et al.  Estimation of the burden of active and life-time epilepsy: A meta-analytic approach , 2010, Epilepsia.

[80]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

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

[82]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[83]  S. Horvath,et al.  Functional organization of the transcriptome in human brain , 2008, Nature Neuroscience.

[84]  W. Löscher,et al.  Increase in antiepileptic efficacy during prolonged treatment with valproic acid: Role of inhibition of histone deacetylases? , 2008, Epilepsy Research.

[85]  Giuseppe Biagini,et al.  The pilocarpine model of temporal lobe epilepsy , 2008, Journal of Neuroscience Methods.

[86]  S. Kulkarni,et al.  Effect of Withania somnifera Dunal root extract against pentylenetetrazol seizure threshold in mice: possible involvement of GABAergic system. , 2008, Indian journal of experimental biology.

[87]  Bin Zhang,et al.  Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R , 2008, Bioinform..

[88]  Terry M. Therneau,et al.  What Does PLIER Really Do? , 2008, Cancer informatics.

[89]  Peter Langfelder,et al.  Eigengene networks for studying the relationships between co-expression modules , 2007, BMC Systems Biology.

[90]  Johanna S. Hardin,et al.  A robust measure of correlation between two genes on a microarray , 2007, BMC Bioinformatics.

[91]  Hiroyuki Miyamoto,et al.  Nav1.1 Localizes to Axons of Parvalbumin-Positive Inhibitory Interneurons: A Circuit Basis for Epileptic Seizures in Mice Carrying an Scn1a Gene Mutation , 2007, The Journal of Neuroscience.

[92]  A. Barabasi,et al.  The human disease network , 2007, Proceedings of the National Academy of Sciences.

[93]  Pall I. Olason,et al.  A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.

[94]  Rickard Sandberg,et al.  Improved precision and accuracy for microarrays using updated probe set definitions , 2007, BMC Bioinformatics.

[95]  Avtar Roopra,et al.  2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP–dependent metabolic regulation of chromatin structure , 2006, Nature Neuroscience.

[96]  Yongjin Li,et al.  Discovering disease-genes by topological features in human protein-protein interaction network , 2006, Bioinform..

[97]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[98]  Dominique Schneider,et al.  Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli , 2006, BMC Genomics.

[99]  Paul A. Bates,et al.  Global topological features of cancer proteins in the human interactome , 2006, Bioinform..

[100]  Xuesong Lu,et al.  The effect of GeneChip gene definitions on the microarray study of cancers. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[101]  J. Mesirov,et al.  GenePattern 2.0 , 2006, Nature Genetics.

[102]  R. Myers,et al.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data , 2005, Nucleic acids research.

[103]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[104]  Bart De Moor,et al.  BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis , 2005, Bioinform..

[105]  G. Mandel,et al.  REST and Its Corepressors Mediate Plasticity of Neuronal Gene Chromatin throughout Neurogenesis , 2005, Cell.

[106]  Matthew W. Hahn,et al.  Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. , 2005, Molecular biology and evolution.

[107]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[108]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[109]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[110]  Martin Vingron,et al.  Variance stabilization applied to microarray data calibration and to the quantification of differential expression , 2002, ISMB.

[111]  Mathew W. Wright,et al.  Guidelines for human gene nomenclature. , 2002, Genomics.

[112]  W. Löscher.  Basic Pharmacology of Valproate , 2002 .

[113]  W. Löscher.  Basic pharmacology of valproate: a review after 35 years of clinical use for the treatment of epilepsy. , 2002, CNS drugs.

[114]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[115]  K. Christensen,et al.  Genetic and environmental factors in epilepsy: a population-based study of 11 900 Danish twin pairs , 2001, Epilepsy Research.

[116]  S. Berkovic,et al.  Epilepsies in twins: Genetics of the major epilepsy syndromes , 1998, Annals of neurology.

[117]  J. Meyer,et al.  Univariate genetic analyses of epilepsy and seizures in a population‐based twin study: The Virginia twin registry , 1998, Genetic epidemiology.

[118]  F. Dudek,et al.  Neuron loss, granule cell axon reorganization, and functional changes in the dentate gyrus of epileptic kainate-treated rats. , 1997, The Journal of comparative neurology.

[119]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[120]  W. Hauser,et al.  Incidence of Epilepsy and Unprovoked Seizures in Rochester, Minnesota: 1935–1984 , 1993, Epilepsia.

[121]  J. H. Kim,et al.  Hippocampal interneuron loss and plasticity in human temporal lobe epilepsy , 1989, Brain Research.

[122]  M. DePamphilis,et al.  HUMAN DISEASE , 1957, The Ulster Medical Journal.