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Genome-scale transcriptional regulatory network models for the mouse and human striatum predict roles for SMAD3 and other transcription factors in Huntington’s disease

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1 of the 71 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-04): 10.7554/elife.12248 (notice 2018-04-12).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471142727.mb2131s110openalex-snapshot

Mapping Regulatory Factors by Immunoprecipitation from Native Chromatin

inferredcites →https://doi.org/10.1006/exnr.1999.7170openalex-snapshot

Increased Complement Biosynthesis By Microglia and Complement Activation on Neurons in Huntington's Disease

inferredcites →https://doi.org/10.1007/s00702-014-1293-0openalex-snapshot

Common mechanisms in neurodegeneration and neuroinflammation: a BrainNet Europe gene expression microarray study

inferredcites →https://doi.org/10.1007/s12035-016-0010-4openalex-snapshot

Genome-wide Analysis of RARβ Transcriptional Targets in Mouse Striatum Links Retinoic Acid Signaling with Huntington’s Disease and Other Neurodegenerative Disorders

inferredcites →https://doi.org/10.1016/0092-8674(93)90585-eopenalex-snapshot

A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes

inferredcites →https://doi.org/10.1016/j.brainresbull.2011.10.001openalex-snapshot

Longitudinal analysis of gene expression and behaviour in the HdhQ150 mouse model of Huntington's disease

inferredcites →https://doi.org/10.1016/j.cell.2008.10.029openalex-snapshot

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

inferredcites →https://doi.org/10.1016/j.cell.2012.12.009openalex-snapshot

DNA-Binding Specificities of Human Transcription Factors

inferredcites →https://doi.org/10.1016/j.cels.2016.06.006openalex-snapshot

Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis

inferredcites →https://doi.org/10.1016/j.molcel.2010.01.030openalex-snapshot

Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State

inferredcites →https://doi.org/10.1016/j.nbd.2011.07.001openalex-snapshot

What have we learned from gene expression profiles in Huntington's disease?

inferredcites →https://doi.org/10.1016/j.nbd.2013.08.009openalex-snapshot

Loss of corticostriatal and thalamostriatal synaptic terminals precedes striatal projection neuron pathology in heterozygous Q140 Huntington's disease mice

inferredcites →https://doi.org/10.1016/j.neuron.2012.05.024openalex-snapshot

Network Organization of the Huntingtin Proteomic Interactome in Mammalian Brain

inferredcites →https://doi.org/10.1016/j.neuroscience.2015.10.039openalex-snapshot

Pathological gamma oscillations, impaired dopamine release, synapse loss and reduced dynamic range of unitary glutamatergic synaptic transmission in the striatum of hypokinetic Q175 Huntington mice

inferredcites →https://doi.org/10.1016/j.stemcr.2015.11.005openalex-snapshot

Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in Human Huntington’s Disease Neural Stem Cells

inferredcites →https://doi.org/10.1016/s1474-4422(13)70088-7openalex-snapshot

Predictors of phenotypic progression and disease onset in premanifest and early-stage Huntington's disease in the TRACK-HD study: analysis of 36-month observational data

inferredcites →https://doi.org/10.1038/75556openalex-snapshot

Gene Ontology: tool for the unification of biology

inferredcites →https://doi.org/10.1038/nature11212openalex-snapshot

An expansive human regulatory lexicon encoded in transcription factor footprints

inferredcites →https://doi.org/10.1038/nature11245openalex-snapshot

Architecture of the human regulatory network derived from ENCODE data

inferredcites →https://doi.org/10.1038/nature13992openalex-snapshot

A comparative encyclopedia of DNA elements in the mouse genome

inferredcites →https://doi.org/10.1038/nbt.3587openalex-snapshot

Large-scale phenome analysis defines a behavioral signature for Huntington's disease genotype in mice

inferredcites →https://doi.org/10.1038/ng1219openalex-snapshot

Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes

inferredcites →https://doi.org/10.1038/nm.4003openalex-snapshot

PPAR-δ is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.2016openalex-snapshot

Wisdom of crowds for robust gene network inference

inferredcites →https://doi.org/10.1038/nn.4256openalex-snapshot

Integrated genomics and proteomics define huntingtin CAG length–dependent networks in mice

inferredcites →https://doi.org/10.1073/pnas.0804249105openalex-snapshot

The HDAC inhibitor 4b ameliorates the disease phenotype and transcriptional abnormalities in Huntington's disease transgenic mice

inferredcites →https://doi.org/10.1089/106652700750050961openalex-snapshot

Using Bayesian Networks to Analyze Expression Data

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btq466openalex-snapshot

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

inferredcites →https://doi.org/10.1093/bioinformatics/btr064openalex-snapshot

FIMO: scanning for occurrences of a given motif

inferredcites →https://doi.org/10.1093/hmg/8.1.115openalex-snapshot

Length-dependent gametic CAG repeat instability in the Huntington's disease knock-in mouse

inferredcites →https://doi.org/10.1093/hmg/9.4.503openalex-snapshot

Long glutamine tracts cause nuclear localization of a novel form of huntingtin in medium spiny striatal neurons in HdhQ92 and HdhQ111 knock-in mice

inferredcites →https://doi.org/10.1093/hmg/9.9.1259openalex-snapshot

Decreased expression of striatal signaling genes in a mouse model of Huntington's disease

inferredcites →https://doi.org/10.1093/hmg/ddl013openalex-snapshot

Regional and cellular gene expression changes in human Huntington's disease brain

inferredcites →https://doi.org/10.1093/hmg/ddm133openalex-snapshot

Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage

inferredcites →https://doi.org/10.1093/hmg/ddp524openalex-snapshot

Huntingtin facilitates polycomb repressive complex 2

inferredcites →https://doi.org/10.1093/hmg/ddq018openalex-snapshot

Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis

inferredcites →https://doi.org/10.1093/hmg/ddr355openalex-snapshot

Differential effects of the Huntington's disease CAG mutation in striatum and cerebellum are quantitative not qualitative

inferredcites →https://doi.org/10.1093/hmg/dds132openalex-snapshot

Forkhead box protein p1 is a transcriptional repressor of immune signaling in the CNS: implications for transcriptional dysregulation in Huntington disease

inferredcites →https://doi.org/10.1093/hmg/ddt036openalex-snapshot

A critical role of astrocyte-mediated nuclear factor-κB-dependent inflammation in Huntington's disease

inferredcites →https://doi.org/10.1093/nar/gkj143openalex-snapshot

TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes

inferredcites →https://doi.org/10.1093/nar/gkq130openalex-snapshot

Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells

inferredcites →https://doi.org/10.1093/nar/gks1123openalex-snapshot

TFClass: an expandable hierarchical classification of human transcription factors

inferredcites →https://doi.org/10.1093/nar/gks433openalex-snapshot

Inferring direct DNA binding from ChIP-seq

inferredcites →https://doi.org/10.1093/nar/gkt850openalex-snapshot

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

inferredcites →https://doi.org/10.1093/nar/gkt997openalex-snapshot

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

inferredcites →https://doi.org/10.1093/nar/gku1045openalex-snapshot

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

inferredcites →https://doi.org/10.1093/nar/gku463openalex-snapshot

ChIP-Enrich: gene set enrichment testing for ChIP-seq data

inferredcites →https://doi.org/10.1093/nar/gkv300openalex-snapshot

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

inferredcites →https://doi.org/10.1097/00005072-198511000-00003openalex-snapshot

Neuropathological Classification of Huntingtonʼs Disease

inferredcites →https://doi.org/10.1111/j.1582-4934.2010.01011.xopenalex-snapshot

Early defect of transforming growth factor β1 formation in Huntington’s disease

inferredcites →https://doi.org/10.1111/j.2517-6161.1996.tb02080.xopenalex-snapshot

Regression Shrinkage and Selection Via the Lasso

inferredcites →https://doi.org/10.1155/2011/124256openalex-snapshot

Transforming Growth Factor-Beta Signaling in the Neural Stem Cell Niche: A Therapeutic Target for Huntington's Disease

inferredcites →https://doi.org/10.1186/1471-2105-7-s1-s7openalex-snapshot

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

inferredcites →https://doi.org/10.1186/1752-0509-6-145openalex-snapshot

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

inferredcites →https://doi.org/10.1186/gb-2006-7-5-r36openalex-snapshot

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1371/journal.pone.0012776openalex-snapshot

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

inferredcites →https://doi.org/10.1371/journal.pone.0123527openalex-snapshot

Characterization of HTT Inclusion Size, Location, and Timing in the zQ175 Mouse Model of Huntington´s Disease: An In Vivo High-Content Imaging Study

inferredcites →https://doi.org/10.1523/jneurosci.0277-12.2012openalex-snapshot

Integration of β-Catenin, Sirtuin, and FOXO Signaling Protects from Mutant Huntingtin Toxicity

inferredcites →https://doi.org/10.1523/jneurosci.1860-14.2014openalex-snapshot

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

inferredcites →https://doi.org/10.1523/jneurosci.2126-08.2008openalex-snapshot

Huntingtin Modulates Transcription, Occupies Gene PromotersIn Vivo, and Binds Directly to DNA in a Polyglutamine-Dependent Manner

inferredcites →https://doi.org/10.1523/jneurosci.2986-07.2008openalex-snapshot

Ctip2Controls the Differentiation of Medium Spiny Neurons and the Establishment of the Cellular Architecture of the Striatum

inferredcites →https://doi.org/10.1523/jneurosci.3355-05.2005openalex-snapshot

Dysfunction of the Cholesterol Biosynthetic Pathway in Huntington's Disease

inferredcites →https://doi.org/10.1523/jneurosci.3842-04.2005openalex-snapshot

Disintegration of the Sleep-Wake Cycle and Circadian Timing in Huntington's Disease

inferredcites →https://doi.org/10.1523/jneurosci.4278-06.2007openalex-snapshot

Widespread Disruption of Repressor Element-1 Silencing Transcription Factor/Neuron-Restrictive Silencer Factor Occupancy at Its Target Genes in Huntington's Disease

inferredcites →https://doi.org/10.18637/jss.v033.i01openalex-snapshot

Regularization Paths for Generalized Linear Models via Coordinate Descent

inferredcites →https://doi.org/10.7554/elife.12248openalex-snapshot

RETRACTED: A mathematical model explains saturating axon guidance responses to molecular gradients

inferredcites →https://doi.org/10.7554/elife.17056openalex-snapshot

Real-time imaging of Huntingtin aggregates diverting target search and gene transcription

inferredcites →https://doi.org/10.7916/d8g15zbpopenalex-snapshot

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/1878-0261.12320openalex-snapshot

Targeting TWIST 1 through loss of function inhibits tumorigenicity of human glioblastoma

inferred← citeshttps://doi.org/10.1016/j.nbd.2018.09.005openalex-snapshot

Motor neuron loss and neuroinflammation in a model of α-synuclein-induced neurodegeneration

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