Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity

Genetics and Molecular Pathogenesis of Gastric Adenocarcinoma

(2015) Patrick Tan et al.   GASTROENTEROLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes

(2015) Razvan Cristescu et al.   NATURE MEDICINE

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

High-throughput genotyping of CRISPR/Cas9-mediated mutants using fluorescent PCR-capillary gel electrophoresis

(2015) Muhammad Khairul Ramlee et al.   Scientific Reports

MALAT1 promotes cell proliferation in gastric cancer by recruiting SF2/ASF

(2014) Junqing Wang et al.   BIOMEDICINE & PHARMACOTHERAPY

Mutually exclusive FGFR2, HER2, and KRAS gene amplifications in gastric cancer revealed by multicolour FISH

(2014) Kakoli Das et al.   CANCER LETTERS

Epithelial–mesenchymal transition confers resistance to selective FGFR inhibitors in SNU-16 gastric cancer cells

(2014) Paulina Grygielewicz et al.   Gastric Cancer

Regulatory crosstalk between lineage-survival oncogenesKLF5, GATA4andGATA6cooperatively promotes gastric cancer development

(2014) Na-Yu Chia et al.   GUT

Demonstration of the usefulness of epigenetic cancer risk prediction by a multicentre prospective cohort study

(2014) Kiyoshi Asada et al.   GUT

Clinical Significance of POU5F1P1 rs10505477 Polymorphism in Chinese Gastric Cancer Patients Receving Cisplatin-Based Chemotherapy after Surgical Resection

(2014) Lili Shen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Increased expression of long noncoding RNA ABHD11-AS1 in gastric cancer and its clinical significance

(2014) Xinxiu Lin et al.   MEDICAL ONCOLOGY

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Elf3 drives β-catenin transactivation and associates with poor prognosis in colorectal cancer

(2014) J-L Wang et al.   Cell Death & Disease

Nanoscale chromatin profiling of gastric adenocarcinoma reveals cancer-associated cryptic promoters and somatically acquired regulatory elements

(2014) Masafumi Muratani et al.   Nature Communications

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity

(2013) B. Zhang et al.   GENOME RESEARCH

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

(2013) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Association of the Autoimmune Disease Scleroderma with an Immunologic Response to Cancer

(2013) C. G. Joseph et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

Accurate estimation of short read mapping quality for next-generation genome sequencing

(2012) M. Ruffalo et al.   BIOINFORMATICS

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

(2012) Jingli A. Zhang et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Long noncoding RNA CCAT1, which could be activated by c-Myc, promotes the progression of gastric carcinoma

(2012) Feng Yang et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding

(2012) M. P. Verzi et al.   MOLECULAR AND CELLULAR BIOLOGY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

(2012) Zhi Jiang Zang et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

Methylation Subtypes and Large-Scale Epigenetic Alterations in Gastric Cancer

(2012) H. Zouridis et al.   Science Translational Medicine

Gastric intestinal metaplasia revisited: function and regulation of CDX2

(2012) Rita Barros et al.   TRENDS IN MOLECULAR MEDICINE

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

(2012) Aaron Diaz et al.   GENOME BIOLOGY

Intrinsic Subtypes of Gastric Cancer, Based on Gene Expression Pattern, Predict Survival and Respond Differently to Chemotherapy

(2011) Iain Beehuat Tan et al.   GASTROENTEROLOGY

Claudin-4 overexpression is associated with epigenetic derepression in gastric carcinoma

(2011) Mi Jeong Kwon et al.   LABORATORY INVESTIGATION

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

(2011) Kai Wang et al.   NATURE GENETICS

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Gene Expression Profiling of Metaplastic Lineages Identifies CDH17 as a Prognostic Marker in Early Stage Gastric Cancer

(2010) Hyuk–Joon Lee et al.   GASTROENTEROLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology