Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance

(2016) Richard Marcotte et al.   CELL

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

(2015) Minho Chae et al.   BMC BIOINFORMATICS

Aberrantly expressed Fra-1 by IL-6/STAT3 transactivation promotes colorectal cancer aggressiveness through epithelial–mesenchymal transition

(2015) Hong Liu et al.   CARCINOGENESIS

No Driver behind the Wheel? Targeting Transcription in Cancer

(2015) Hector L. Franco et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites to Alter the Breast Cancer Cell Transcriptome

(2015) Hector L. Franco et al.   MOLECULAR CELL

Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells

(2015) Miao Sun et al.   MOLECULAR CELL

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs

(2015) Nasun Hah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses

(2014) Xin Luo et al.   BMC GENOMICS

Genome-wide Profiling of AP-1-Regulated Transcription Provides Insights into the Invasiveness of Triple-Negative Breast Cancer

(2014) C. Zhao et al.   CANCER RESEARCH

CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer

(2014) Edmond Chipumuro et al.   CELL

Fra-1/AP-1 induces EMT in mammary epithelial cells by modulating Zeb1/2 and TGFβ expression

(2014) L Bakiri et al.   CELL DEATH AND DIFFERENTIATION

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

FRA-1 as a driver of tumour heterogeneity: a nexus between oncogenes and embryonic signalling pathways in cancer

(2014) A S Dhillon et al.   ONCOGENE

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells

(2014) Jeannine Diesch et al.   PLoS One

Transcription factor PREP1 induces EMT and metastasis by controlling the TGF- -SMAD3 pathway in non-small cell lung adenocarcinoma

(2014) M. Risolino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers

(2013) Ulf Andersson Ørom et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

FOXC1 regulates the functions of human basal-like breast cancer cells by activating NF-κB signaling

(2012) J Wang et al.   ONCOGENE

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

GOBO: Gene Expression-Based Outcome for Breast Cancer Online

(2011) Markus Ringnér et al.   PLoS One

Forkhead transcription factors: key players in health and disease

(2011) Bérénice A. Benayoun et al.   TRENDS IN GENETICS

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

(2010) Heng Li et al.   BIOINFORMATICS

FOXC1 Is a Potential Prognostic Biomarker with Functional Significance in Basal-like Breast Cancer

(2010) P. S. Ray et al.   CANCER RESEARCH

AP-1 — The Jun proteins: Oncogenes or tumor suppressors in disguise?

(2010) Eitan Shaulian   CELLULAR SIGNALLING

FOXA1 is an essential determinant of ER  expression and mammary ductal morphogenesis

(2010) G. M. Bernardo et al.   DEVELOPMENT

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Gene-Expression Signatures in Breast Cancer

(2009) Christos Sotiriou et al.   NEW ENGLAND JOURNAL OF MEDICINE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE