MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data

A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy

(2020) Nadia Khan et al.   PLoS One

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

(2019) Alexandra B Keenan et al.   NUCLEIC ACIDS RESEARCH

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

(2018) Zhenjia Wang et al.   BIOINFORMATICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons

(2018) Baptiste N. Jaeger et al.   Nature Communications

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc

(2016) Dev Sharan Sams et al.   Cell Reports

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

(2016) Raphaël Mourad et al.   PLoS Computational Biology

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Sp3/REST/HDAC1/HDAC2 Complex Represses and Sp1/HIF-1/p300 Complex Activates ncx1 Gene Transcription, in Brain Ischemia and in Ischemic Brain Preconditioning, by Epigenetic Mechanism

(2015) L. Formisano et al.   JOURNAL OF NEUROSCIENCE

Type 1 Insulin-Like Growth Factor Receptor/Insulin Receptor Substrate 1 Signaling Confers Pathogenic Activity on Breast Tumor Cells Lacking REST

(2015) Kassondra Meyer et al.   MOLECULAR AND CELLULAR BIOLOGY

The Neuronal Activity-Driven Transcriptome

(2014) Eva Benito et al.   MOLECULAR NEUROBIOLOGY

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype

(2014) James C McGann et al.   eLife

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

Induction of the RNA Regulator LIN28A Is Required for the Growth and Pathogenesis of RESTless Breast Tumors

(2012) K. T. W. Gunsalus et al.   CANCER RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

(2012) Nikolaj Dietrich et al.   PLoS Genetics

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

A Comparison of PAM50 Intrinsic Subtyping with Immunohistochemistry and Clinical Prognostic Factors in Tamoxifen-Treated Estrogen Receptor-Positive Breast Cancer

(2010) T. O. Nielsen et al.   CLINICAL CANCER RESEARCH

Cell type specificity of chromatin organization mediated by CTCF and cohesin

(2010) Chunhui Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcription Factor REST Is Lost in Aggressive Breast Cancer

(2010) Matthew P. Wagoner et al.   PLoS Genetics

C-Fos expression is a molecular predictor of progression and survival in epithelial ovarian carcinoma

(2008) S Mahner et al.   BRITISH JOURNAL OF CANCER