A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

[1]  R. Elkon,et al.  A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis , 2021, Genome Biology.

[2]  Wenquan Wang,et al.  The role of collagen in cancer: from bench to bedside , 2019, Journal of Translational Medicine.

[3]  T. Huang,et al.  A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer. , 2019, Molecular cell.

[4]  Yifang Zhou,et al.  Overexpression of KIF18A promotes cell proliferation, inhibits apoptosis, and independently predicts unfavorable prognosis in lung adenocarcinoma , 2019, IUBMB life.

[5]  Chunling Yi,et al.  YAP/TAZ Signaling and Resistance to Cancer Therapy. , 2019, Trends in cancer.

[6]  Fa-Xing Yu,et al.  GPCR-Hippo Signaling in Cancer , 2019, Cells.

[7]  Yanyan Han Analysis of the role of the Hippo pathway in cancer , 2019, Journal of Translational Medicine.

[8]  H. G. van der Poel,et al.  Optimized ChIP-seq method facilitates transcription factor profiling in human tumors , 2018, Life Science Alliance.

[9]  P. Sun,et al.  Hippo-YAP pathway mediated resistance to crizotinib in ROS1-positive lung cancer. , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[10]  G. Xiong,et al.  Membrane associated collagen XIII promotes cancer metastasis and enhances anoikis resistance , 2018, Breast Cancer Research.

[11]  Xiaodong Zhang,et al.  The role of YAP/TAZ activity in cancer metabolic reprogramming , 2018, Molecular Cancer.

[12]  Y. Shyr,et al.  Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation , 2018, BMC genomics.

[13]  R. Elkon,et al.  Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence , 2018, Genome Biology.

[14]  Xiao-lan Li,et al.  Hippo component YAP promotes focal adhesion and tumour aggressiveness via transcriptionally activating THBS1/FAK signalling in breast cancer , 2018, Journal of experimental & clinical cancer research : CR.

[15]  R. Eisenman,et al.  The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis , 2018, Frontiers of Medicine.

[16]  S. Piccolo,et al.  YAP/TAZ upstream signals and downstream responses , 2018, Nature Cell Biology.

[17]  Víctor Quesada,et al.  nVenn: generalized, quasi‐proportional Venn and Euler diagrams , 2018, Bioinform..

[18]  D. Hwang,et al.  YAP/TAZ Initiates Gastric Tumorigenesis via Upregulation of MYC. , 2018, Cancer research.

[19]  Yuchen Liu,et al.  Enhancer RNAs (eRNAs): New Insights into Gene Transcription and Disease Treatment , 2018, Journal of Cancer.

[20]  Zhi-yan Hu,et al.  FSTL1 interacts with VIM and promotes colorectal cancer metastasis via activating the focal adhesion signalling pathway , 2018, Cell Death & Disease.

[21]  Sabrina Strano,et al.  YAP and TAZ in Lung Cancer: Oncogenic Role and Clinical Targeting , 2018, Cancers.

[22]  Adrian V. Lee,et al.  An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics , 2018, Cell.

[23]  S. Myung,et al.  Clinical implications of the Hippo-YAP pathway in multiple cancer contexts , 2018, BMB reports.

[24]  S. Bae,et al.  DNA binding partners of YAP/TAZ , 2018, BMB reports.

[25]  Jimyung Seo,et al.  Regulation of Hippo signaling by actin remodeling , 2018, BMB reports.

[26]  Jun Yu Li,et al.  Synaptopodin‐2 suppresses metastasis of triple‐negative breast cancer via inhibition of YAP/TAZ activity , 2017, The Journal of pathology.

[27]  K. Chan,et al.  FSTL1 Promotes Metastasis and Chemoresistance in Esophageal Squamous Cell Carcinoma through NFκB-BMP Signaling Cross-talk. , 2017, Cancer research.

[28]  P. Jeannesson,et al.  Collagen type 1 promotes survival of human breast cancer cells by overexpressing Kv10.1 potassium and Orai1 calcium channels through DDR1-dependent pathway , 2017, Oncotarget.

[29]  D. Broide,et al.  Autophagy plays a role in FSTL1-induced epithelial mesenchymal transition and airway remodeling in asthma. , 2017, American journal of physiology. Lung cellular and molecular physiology.

[30]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[31]  R. John,et al.  Mini review: Multifaceted role played by cyclin D1 in tumor behavior , 2017, Indian journal of dental research : official publication of Indian Society for Dental Research.

[32]  J. Diehl,et al.  Cyclin D1, cancer progression, and opportunities in cancer treatment , 2016, Journal of Molecular Medicine.

[33]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[34]  T. Chong,et al.  Elevated expression of KIF18A enhances cell proliferation and predicts poor survival in human clear cell renal carcinoma. , 2016, Experimental and therapeutic medicine.

[35]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[36]  Stefano Piccolo,et al.  YAP/TAZ at the Roots of Cancer. , 2016, Cancer cell.

[37]  B. Thompson,et al.  YAP and TAZ in epithelial stem cells: A sensor for cell polarity, mechanical forces and tissue damage , 2016, BioEssays : news and reviews in molecular, cellular and developmental biology.

[38]  Xiaolong Yang,et al.  Roles of the Hippo pathway in lung development and tumorigenesis , 2016, International journal of cancer.

[39]  R. Elkon,et al.  Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9 , 2016, Nature Biotechnology.

[40]  G. G. Galli,et al.  YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers. , 2015, Molecular cell.

[41]  K. Guan,et al.  YAP and TAZ: a nexus for Hippo signaling and beyond. , 2015, Trends in cell biology.

[42]  Antonio Rosato,et al.  Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth , 2015, Nature Cell Biology.

[43]  N. Luo,et al.  Overexpression of TMEM158 contributes to ovarian carcinogenesis , 2015, Journal of experimental & clinical cancer research : CR.

[44]  J. Palacios,et al.  Nuclear TAZ expression associates with the triple-negative phenotype in breast cancer. , 2015, Endocrine-related cancer.

[45]  N. Hanley,et al.  TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors , 2015, Nature Cell Biology.

[46]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[47]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[48]  Jun S. Liu,et al.  MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens , 2014, Genome Biology.

[49]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[50]  S. Dupont,et al.  The biology of YAP/TAZ: hippo signaling and beyond. , 2014, Physiological reviews.

[51]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[52]  Philipp J. Keller,et al.  Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data , 2014, Nature Methods.

[53]  R. Shiekhattar,et al.  Enhancer RNAs: the new molecules of transcription. , 2014, Current opinion in genetics & development.

[54]  Jing Zhao,et al.  Overexpression of YAP1 is Correlated with Progression, Metastasis and Poor Prognosis in Patients with Gastric Carcinoma , 2014, Pathology & Oncology Research.

[55]  J. Foekens,et al.  Hallmarks of aromatase inhibitor drug resistance revealed by epigenetic profiling in breast cancer. , 2013, Cancer research.

[56]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[57]  F. Zhou,et al.  Overexpression of YAP 1 contributes to progressive features and poor prognosis of human urothelial carcinoma of the bladder , 2013, BMC Cancer.

[58]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[59]  E. Rutgers,et al.  A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples , 2013, BMC Genomics.

[60]  David M. Thomas,et al.  The Hippo pathway and human cancer , 2013, Nature Reviews Cancer.

[61]  Justin Guinney,et al.  GSVA: gene set variation analysis for microarray and RNA-Seq data , 2013, BMC Bioinformatics.

[62]  Y. Kondo,et al.  YAP induces malignant mesothelioma cell proliferation by upregulating transcription of cell cycle-promoting genes , 2012, Oncogene.

[63]  R. Pestell,et al.  Cyclins and cell cycle control in cancer and disease. , 2012, Genes & cancer.

[64]  Hoguen Kim,et al.  Nuclear expression of Yes-associated protein 1 correlates with poor prognosis in intestinal type gastric cancer. , 2012, Anticancer research.

[65]  Chi V Dang,et al.  MYC on the Path to Cancer , 2012, Cell.

[66]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[67]  S. Bicciato,et al.  The Hippo Transducer TAZ Confers Cancer Stem Cell-Related Traits on Breast Cancer Cells , 2011, Cell.

[68]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[69]  J. Mpindi,et al.  Vimentin regulates EMT induction by Slug and oncogenic H-Ras and migration by governing Axl expression in breast cancer , 2011, Oncogene.

[70]  Jun Yu,et al.  Yes-Associated Protein 1 Exhibits Oncogenic Property in Gastric Cancer and Its Nuclear Accumulation Associates with Poor Prognosis , 2011, Clinical Cancer Research.

[71]  G. Halder,et al.  Hippo signaling: growth control and beyond , 2011, Development.

[72]  D. Pan,et al.  The hippo signaling pathway in development and cancer. , 2010, Developmental cell.

[73]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[74]  M. Groudine,et al.  Enhancers: the abundance and function of regulatory sequences beyond promoters. , 2010, Developmental biology.

[75]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[76]  Eva Hoffmann,et al.  The synaptonemal complex protein, Zip1, promotes the segregation of nonexchange chromosomes at meiosis I , 2009, Proceedings of the National Academy of Sciences.

[77]  D. Dawson,et al.  The Synaptonemal Complex Protein Zip1 Promotes Bi-Orientation of Centromeres at Meiosis I , 2009, PLoS genetics.

[78]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[79]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[80]  Zhengyu Zha,et al.  TAZ Promotes Cell Proliferation and Epithelial-Mesenchymal Transition and Is Inhibited by the Hippo Pathway , 2008, Molecular and Cellular Biology.

[81]  Li Li,et al.  Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control. , 2007, Genes & development.

[82]  G. Feldmann,et al.  Elucidation of a Universal Size-Control Mechanism in Drosophila and Mammals , 2007, Cell.

[83]  Johanna Ivaska,et al.  Novel functions of vimentin in cell adhesion, migration, and signaling. , 2007, Experimental cell research.

[84]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[85]  Jianmin Zhang,et al.  Transforming properties of YAP, a candidate oncogene on the chromosome 11q22 amplicon , 2006, Proceedings of the National Academy of Sciences.

[86]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[87]  L. Sakai,et al.  Prolyl 3-Hydroxylase 1, Enzyme Characterization and Identification of a Novel Family of Enzymes* , 2004, Journal of Biological Chemistry.

[88]  D. Brenner,et al.  TRAM2 Protein Interacts with Endoplasmic Reticulum Ca2+ Pump Serca2b and Is Necessary for Collagen Type I Synthesis , 2004, Molecular and Cellular Biology.

[89]  Shian Wu,et al.  hippo Encodes a Ste-20 Family Protein Kinase that Restricts Cell Proliferation and Promotes Apoptosis in Conjunction with salvador and warts , 2003, Cell.

[90]  I. Hariharan,et al.  The Drosophila Mst Ortholog, hippo, Restricts Growth and Cell Proliferation and Promotes Apoptosis , 2003, Cell.

[91]  R. Gray Modeling Survival Data: Extending the Cox Model , 2002 .

[92]  M. Eilers,et al.  Control of cell proliferation by Myc. , 1998, Trends in cell biology.

[93]  B. Jungnickel,et al.  Signal sequence-dependent function of the TRAM protein during early phases of protein transport across the endoplasmic reticulum membrane , 1996, The Journal of cell biology.

[94]  T. Rapoport,et al.  Protein translocation into proteoliposomes reconstituted from purified components of the endoplasmic reticulum membrane , 1993, Cell.

[95]  M. Pagano,et al.  Cyclin D1 is a nuclear protein required for cell cycle progression in G1. , 1993, Genes & development.

[96]  G. Roeder,et al.  ZIP1 is a synaptonemal complex protein required for meiotic chromosome synapsis , 1993, Cell.

[97]  T. Rapoport,et al.  A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation , 1992, Cell.

[98]  G. Blobel,et al.  Social function of adult men with attention-deficit/hyperactivity disorder in the context of military service , 2018, Neuropsychiatric disease and treatment.

[99]  G. Blobel,et al.  Translocation of proteins across the endoplasmic reticulum. I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein , 1981, The Journal of cell biology.

[100]  Florian Hahne,et al.  Visualizing Genomic Data Using Gviz and Bioconductor , 2016, Statistical Genomics.

[101]  A. Dreher Modeling Survival Data Extending The Cox Model , 2016 .

[102]  J. Olsen,et al.  Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity. , 2016, Methods in molecular biology.

[103]  K. Guan,et al.  A coordinated phosphorylation by Lats and CK1 regulates YAP stability through SCF(beta-TRCP). , 2010, Genes & development.

[104]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[105]  P. Walter Protein translocation. Travelling by TRAM. , 1992, Nature.