Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma

[1]  Lipeng Chen,et al.  Targeting EFNA1 suppresses tumor progression via the cMYC-modulated cell cycle and autophagy in esophageal squamous cell carcinoma , 2023, Discover Oncology.

[2]  A. Bass,et al.  Improving outcomes in patients with oesophageal cancer , 2023, Nature Reviews Clinical Oncology.

[3]  Hui‐Ming Yu,et al.  Identification of a three-gene prognostic signature for radioresistant esophageal squamous cell carcinoma , 2023, World journal of clinical oncology.

[4]  Ruifeng Xu,et al.  LncRNA TMPO-AS1 promotes esophageal squamous cell carcinoma progression by forming biomolecular condensates with FUS and p300 to regulate TMPO transcription , 2022, Experimental & Molecular Medicine.

[5]  Bin Huang,et al.  EFNA1 in gastrointestinal cancer: Expression, regulation and clinical significance , 2022, World journal of gastrointestinal oncology.

[6]  J. Ajani,et al.  Adjuvant Nivolumab in Resected Esophageal or Gastroesophageal Junction Cancer. , 2021, The New England journal of medicine.

[7]  A. Jemal,et al.  Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries , 2021, CA: a cancer journal for clinicians.

[8]  Laura H. Tang,et al.  Treatment of Locally Advanced Esophageal Carcinoma: ASCO Guideline. , 2020, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[9]  Jialong Liang,et al.  Inter- and intratumor DNA methylation heterogeneity associated with lymph node metastasis and prognosis of esophageal squamous cell carcinoma , 2020, Theranostics.

[10]  Giovanni Parmigiani,et al.  ComBat-seq: batch effect adjustment for RNA-seq count data , 2020, bioRxiv.

[11]  A. Guo,et al.  ImmuCellAI: A Unique Method for Comprehensive T‐Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy , 2019, bioRxiv.

[12]  B. Haas,et al.  Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods , 2019, Genome Biology.

[13]  Gunnar Rätsch,et al.  A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters , 2019, Cell.

[14]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[15]  O. Abdel-Wahab,et al.  Aberrant RNA Splicing in Cancer. , 2019, Annual review of cancer biology.

[16]  D. Ilson,et al.  Neoadjuvant therapy for esophageal cancer: Who, when, and what? , 2018, Cancer.

[17]  Zhen Yang,et al.  LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases , 2018, Nucleic Acids Res..

[18]  A. Jemal,et al.  Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries , 2018, CA: a cancer journal for clinicians.

[19]  Diego Garrido-Martín,et al.  ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization , 2018, PLoS Comput. Biol..

[20]  Ambrose J. Carr,et al.  Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment , 2018, Cell.

[21]  Kun Zhang,et al.  Transcriptomic signature associated with carcinogenesis and aggressiveness of papillary thyroid carcinoma , 2018, Theranostics.

[22]  Li Ding,et al.  Driver Fusions and Their Implications in the Development and Treatment of Human Cancers , 2018, Cell reports.

[23]  G. Mills,et al.  Comprehensive Characterization of Alternative Polyadenylation in Human Cancer. , 2018, Journal of the National Cancer Institute.

[24]  R. Niu,et al.  A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[25]  Q. Morris,et al.  QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data , 2018, Genome Biology.

[26]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[27]  Wei Li,et al.  3′ UTR lengthening as a novel mechanism in regulating cellular senescence , 2018, Genome research.

[28]  Jesper Lagergren,et al.  Oesophageal cancer , 2017, The Lancet.

[29]  R. Hayes,et al.  Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers. , 2017, Cancer research.

[30]  B. Berman,et al.  Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas , 2017, Gut.

[31]  O. Schwartz,et al.  HEXIM1 and NEAT1 Long Non-coding RNA Form a Multi-subunit Complex that Regulates DNA-Mediated Innate Immune Response. , 2017, Molecular cell.

[32]  M. Dinger,et al.  Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing , 2017, Molecular Cancer Research.

[33]  L. Vermeulen,et al.  Esophageal Adenocarcinoma Cells and Xenograft Tumors Exposed to Erb-b2 Receptor Tyrosine Kinase 2 and 3 Inhibitors Activate Transforming Growth Factor Beta Signaling, Which Induces Epithelial to Mesenchymal Transition. , 2017, Gastroenterology.

[34]  P. He,et al.  SP and KLF Transcription Factors in Digestive Physiology and Diseases. , 2017, Gastroenterology.

[35]  David L. Marron,et al.  Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations , 2017, Nature Communications.

[36]  Ole Christian Lingjærde,et al.  chimeraviz: a tool for visualizing chimeric RNA , 2017, Bioinform..

[37]  Zhiqiao Wang,et al.  Cleavage and polyadenylation: Ending the message expands gene regulation , 2017, RNA biology.

[38]  S. Davis,et al.  Autoreactive T Cells and Chronic Fungal Infection Drive Esophageal Carcinogenesis. , 2017, Cell host & microbe.

[39]  C. Bailey,et al.  The antiproliferative ELF2 isoform, ELF2B, induces apoptosis in vitro and perturbs early lymphocytic development in vivo , 2017, Journal of Hematology & Oncology.

[40]  E. Li,et al.  Integrative analyses of transcriptome sequencing identify novel functional lncRNAs in esophageal squamous cell carcinoma , 2017, Oncogenesis.

[41]  Benjamin J. Raphael,et al.  Integrated genomic characterization of oesophageal carcinoma , 2017, Nature.

[42]  Z. Cai,et al.  HOTTIP: a critical oncogenic long non-coding RNA in human cancers. , 2016, Molecular bioSystems.

[43]  P. Krause,et al.  Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner , 2016, Proceedings of the National Academy of Sciences.

[44]  M. Nöthen,et al.  Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis , 2016, The Lancet. Oncology.

[45]  Eric C. Rouchka,et al.  rMAPS: RNA map analysis and plotting server for alternative exon regulation , 2016, Nucleic Acids Res..

[46]  B. Johansson,et al.  The emerging complexity of gene fusions in cancer , 2015, Nature Reviews Cancer.

[47]  Shengtao Zhu,et al.  Abnormal Localization and Tumor Suppressor Function of Epithelial Tissue-Specific Transcription Factor ESE3 in Esophageal Squamous Cell Carcinoma , 2015, PloS one.

[48]  A. Jemal,et al.  Global cancer statistics, 2012 , 2015, CA: a cancer journal for clinicians.

[49]  Lan Lin,et al.  rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data , 2014, Proceedings of the National Academy of Sciences.

[50]  Wei Li,et al.  Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types , 2014, Nature Communications.

[51]  Hanspeter Pfister,et al.  UpSet: Visualization of Intersecting Sets , 2014, IEEE Transactions on Visualization and Computer Graphics.

[52]  D. Klimstra,et al.  EGFR, HER2 and HER3 dimerization patterns guide targeted inhibition in two histotypes of esophageal cancer , 2014, International journal of cancer.

[53]  Bin Liu,et al.  : Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and , 2010 .

[54]  Hongbing Shen,et al.  Joint analysis of three genome- wide association studies of esophageal squamous cell carcinoma in Chinese populations , 2014 .

[55]  Alexandra Eitel.  Senescence , 2014, British medical journal.

[56]  Qiang Feng,et al.  Identification of genomic alterations in oesophageal squamous cell cancer , 2014, Nature.

[57]  S. Chanock,et al.  A Genome-Wide Association Study Identifies New Susceptibility Loci for Esophageal Adenocarcinoma and Barrett’s Esophagus , 2013, Nature Genetics.

[58]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[59]  R. Elkon,et al.  Alternative cleavage and polyadenylation: extent, regulation and function , 2013, Nature Reviews Genetics.

[60]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[61]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[62]  Howard Y. Chang,et al.  Control of somatic tissue differentiation by the long non-coding RNA TINCR , 2012, Nature.

[63]  Simon C. Potter,et al.  Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett’s esophagus , 2012, Nature Genetics.

[64]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[65]  T. Bailey,et al.  Inferring direct DNA binding from ChIP-seq , 2012, Nucleic acids research.

[66]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[67]  Z. Werb,et al.  The extracellular matrix: A dynamic niche in cancer progression , 2012, The Journal of cell biology.

[68]  Hongbing Shen,et al.  Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations , 2011, Nature Genetics.

[69]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[70]  Hideaki Sugawara,et al.  The Sequence Read Archive , 2010, Nucleic Acids Res..

[71]  Bin Liu,et al.  Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies a susceptibility locus at PLCE1 , 2010, Nature Genetics.

[72]  N. Hu,et al.  A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma , 2010, Nature Genetics.

[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]  F. You,et al.  PCBP2 mediates degradation of the adaptor MAVS via the HECT ubiquitin ligase AIP4 , 2009, Nature Immunology.

[75]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[76]  Y. Kamatani,et al.  Functional variants in ADH1B and ALDH2 coupled with alcohol and smoking synergistically enhance esophageal cancer risk. , 2009, Gastroenterology.

[77]  William Stafford Noble,et al.  Quantifying similarity between motifs , 2007, Genome Biology.

[78]  P. Shannon,et al.  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks , 2003 .

[79]  D. Beer,et al.  Amplification and overexpression of the dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 (DYRK2) gene in esophageal and lung adenocarcinomas. , 2003, Cancer research.

[80]  Jacob D. Jaffe,et al.  Next-generation characterization of the Cancer Cell Line Encyclopedia , 2019, Nature.