Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain

Cancer statistics, 2019

(2019) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding

(2019) Sofia Gkountela et al.   CELL

Transcriptional regulation of normal human mammary cell heterogeneity and its perturbation in breast cancer

(2019) Davide Pellacani et al.   EMBO JOURNAL

TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment

(2019) Lingjie Li et al.   Cell Stem Cell

Molecular Mechanisms of Breast Cancer Metastasis to the Lung: Clinical and Experimental Perspectives

(2019) Braeden Medeiros et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer

(2019) Kening Li et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Normal breast-derived epithelial cells with luminal and intrinsic subtype-enriched gene expression document inter-individual differences in their differentiation cascade

(2018) Brijesh Kumar et al.   CANCER RESEARCH

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

PAM50 Risk of Recurrence Score Predicts 10-Year Distant Recurrence in a Comprehensive Danish Cohort of Postmenopausal Women Allocated to 5 Years of Endocrine Therapy for Hormone Receptor–Positive Early Breast Cancer

(2018) Anne-Vibeke Lænkholm et al.   JOURNAL OF CLINICAL ONCOLOGY

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

(2018) William A. Pastor et al.   NATURE CELL BIOLOGY

Positively selected enhancer elements endow osteosarcoma cells with metastatic competence

(2018) James J Morrow et al.   NATURE MEDICINE

PAM50 for prediction of response to neoadjuvant chemotherapy for ER-positive breast cancer

(2018) Ako Matsushita Ohara et al.   BREAST CANCER RESEARCH AND TREATMENT

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

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

(2017) Hector L. Franco et al.   GENOME RESEARCH

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

The interplay of epigenetic marks during stem cell differentiation and development

(2017) Yaser Atlasi et al.   NATURE REVIEWS GENETICS

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

(2016) Sarah K. Denny et al.   CELL

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks

(2016) Davide Pellacani et al.   Cell Reports

TFAP2C expression in breast cancer: correlation with overall survival beyond 10 years of initial diagnosis

(2015) Susan M. Perkins et al.   BREAST CANCER RESEARCH AND TREATMENT

Metastatic Competence Can Emerge with Selection of Preexisting Oncogenic Alleles without a Need of New Mutations

(2015) Leni S. Jacob et al.   CANCER RESEARCH

PTPRN2 and PLC 1 promote metastatic breast cancer cell migration through PI(4,5)P2-dependent actin remodeling

(2015) C. A. Sengelaub et al.   EMBO JOURNAL

Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery

(2015) Celeste B. Greer et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Mammary stem cells and the differentiation hierarchy: current status and perspectives

(2014) J. E. Visvader et al.   GENES & DEVELOPMENT

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

TFAP2C governs the luminal epithelial phenotype in mammary development and carcinogenesis

(2014) A R Cyr et al.   ONCOGENE

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Data-based filtering for replicated high-throughput transcriptome sequencing experiments

(2013) Andrea Rau et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Collective Invasion in Breast Cancer Requires a Conserved Basal Epithelial Program

(2013) Kevin J. Cheung et al.   CELL

Chromatin modifiers and remodellers: regulators of cellular differentiation

(2013) Taiping Chen et al.   NATURE REVIEWS GENETICS

EMP2 regulates angiogenesis in endometrial cancer cells through induction of VEGF

(2013) L K Gordon et al.   ONCOGENE

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Jetset: selecting the optimal microarray probe set to represent a gene

(2011) Qiyuan Li et al.   BMC BIOINFORMATICS

Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse

(2011) J. Chuck Harrell et al.   BREAST CANCER RESEARCH AND TREATMENT

Basal Breast Cancer: A Complex and Deadly Molecular Subtype

(2011) F. Bertucci et al.   CURRENT MOLECULAR MEDICINE

APOBEC3G promotes liver metastasis in an orthotopic mouse model of colorectal cancer and predicts human hepatic metastasis

(2011) Qingqing Ding et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Genes that mediate breast cancer metastasis to the brain

(2009) Paula D. Bos et al.   NATURE

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Transcriptome Analysis of the Normal Human Mammary Cell Commitment and Differentiation Process

(2008) Afshin Raouf et al.   Cell Stem Cell

Overexpression ofTFAP2Cin invasive breast cancer correlates with a poorer response to anti-hormone therapy and reduced patient survival

(2008) JMW Gee et al.   JOURNAL OF PATHOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY