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Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer†
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Statistical Testing of Shared Genetic Control for Potentially Related Traits
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Smoking and cancer‐related gene expression in bronchial epithelium and non‐small‐cell lung cancers
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Cancer Epigenetics: From Mechanism to Therapy
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The Molecular Taxonomy of Primary Prostate Cancer
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The Functional Impact of Alternative Splicing in Cancer
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FGFR3–TACC3: A novel gene fusion in cervical cancer
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Tumor-specific expression and alternative splicing of the COL6A3 gene in pancreatic cancer
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Intergenically Spliced Chimeric RNAs in Cancer
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Melanocytes as Instigators and Victims of Oxidative Stress
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The Genotype-Tissue Expression (GTEx) project
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MYC: connecting selective transcriptional control to global RNA production
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Pan-cancer analysis of whole genomes
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Cyclin D3 and c-MYC control glucocorticoid-induced cell cycle arrest but not apoptosis in lymphoblastic leukemia cells
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Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer
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Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer
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ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
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Increased sensitivity of melanocytes to oxidative stress and abnormal expression of tyrosinase-related protein in vitiligo
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The Role of Melanin in the Induction of Oxidative DNA Base Damage by Ultraviolet A Irradiation of DNA or Melanoma Cells
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The Biology of Chronic Myeloid Leukemia
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Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma
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A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
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Promoter Choice Influences Alternative Splicing and Determines the Balance of Isoforms Expressed from the Mousebcl-X Gene
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Ovarian Cancer-associated Mutations Disable Catalytic Activity of CDK12, a Kinase That Promotes Homologous Recombination Repair and Resistance to Cisplatin and Poly(ADP-ribose) Polymerase Inhibitors
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IRF-5 Is a Mediator of the Death Receptor-induced Apoptotic Signaling Pathway
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Unanticipated role of melanin in causing carcinogenic cyclobutane pyrimidine dimers
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Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
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BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
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The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btr260openalex-snapshot
Molecular signatures database (MSigDB) 3.0
inferredcites →https://doi.org/10.1093/bioinformatics/btr310openalex-snapshot
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution
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STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
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circlize implements and enhances circular visualization in R
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HTSeq—a Python framework to work with high-throughput sequencing data
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SplAdder : identification, quantification and testing of alternative splicing events from RNA-Seq data
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A weighted exact test for mutually exclusive mutations in cancer
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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
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Gene Ontology Consortium: going forward
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Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex
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The Reactome pathway Knowledgebase
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CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion
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LIMIX: genetic analysis of multiple traits
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iRAP - an integrated RNA-seq Analysis Pipeline
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Machine-learning annotation of human splicing branchpoints
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Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
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The evolutionary history of 2,658 cancers
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The whole-genome panorama of cancer drivers
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Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
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VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
inferredcites →https://doi.org/10.1101/gr.137570.112openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.182899.114openalex-snapshot
Genome-wide discovery of human splicing branchpoints
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A code for transcription initiation in mammalian genomes
inferredcites →https://doi.org/10.1111/bjh.13995openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.1117679openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.1229259openalex-snapshot
Highly Recurrent TERT Promoter Mutations in Human Melanoma
inferredcites →https://doi.org/10.1126/science.1230062openalex-snapshot
TERT Promoter Mutations in Familial and Sporadic Melanoma
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The human transcriptome across tissues and individuals
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A pathology atlas of the human cancer transcriptome
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Signaling through IFN Regulatory Factor-5 Sensitizes p53-Deficient Tumors to DNA Damage–Induced Apoptosis and Cell Death
inferredcites →https://doi.org/10.1158/0008-5472.can-09-2223openalex-snapshot
Nuclear Receptor Coregulators in Cancer Biology
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Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications
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Co-occurring Mutations of Tumor Suppressor Genes, LATS2 and NF2 , in Malignant Pleural Mesothelioma
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Overexpression of KLF13 and FGFR3 in Oral Cancer Cells
inferredcites →https://doi.org/10.1172/jci81522openalex-snapshot
Involvement of activation-induced cytidine deaminase in skin cancer development
inferredcites →https://doi.org/10.1182/blood-2011-04-350579openalex-snapshot
IRF4 mutations in chronic lymphocytic leukemia
inferredcites →https://doi.org/10.1186/1471-2105-11-94openalex-snapshot
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
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Serological identification of Tektin5 as a cancer/testis antigen and its immunogenicity
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ABC transporter activity linked to radiation resistance and molecular subtype in pediatric medulloblastoma
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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
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Tools and best practices for data processing in allelic expression analysis
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The Ensembl Variant Effect Predictor
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MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data
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Poised chromatin in the mammalian germ line
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The birth of new exons: Mechanisms and evolutionary consequences
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Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
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SLX-1 Is Required for Maintaining Genomic Integrity and Promoting Meiotic Noncrossovers in the Caenorhabditis elegans Germline
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Cis and Trans Effects of Human Genomic Variants on Gene Expression
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Alternative Promoters Influence Alternative Splicing at the Genomic Level
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Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
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Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants
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Machine-learning annotation of human splicing branchpoints
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lavaan : An R Package for Structural Equation Modeling
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mediation : R Package for Causal Mediation Analysis
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Rtsne: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
inferredcites →https://doi.org/10.3324/haematol.2010.026831openalex-snapshot
Detection of genomic aberrations in molecularly defined Burkitt's lymphoma by array-based, high resolution, single nucleotide polymorphism analysis
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Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
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SPSS and SAS procedures for estimating indirect effects in simple mediation models
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HER2 Amplification Ratios by Fluorescence In Situ Hybridization and Correlation with Immunohistochemistry in a Cohort of 6556 Breast Cancer Tissues
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SAMD4B, a novel SAM-containing protein, inhibits AP-1-, p53- and p21-mediated transcriptional activity
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Overexpression of collagen VI α3 in gastric cancer
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A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/gepi.22265openalex-snapshot
Powerful rare variant association testing in a copula‐based joint analysis of multiple phenotypes
inferred← citeshttps://doi.org/10.1007/s10555-021-09969-zopenalex-snapshot
Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020
inferred← citeshttps://doi.org/10.1016/j.ccell.2018.07.001openalex-snapshot
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
inferred← citeshttps://doi.org/10.1016/j.cell.2019.08.018openalex-snapshot
A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters
inferred← citeshttps://doi.org/10.1016/j.molcel.2019.12.027openalex-snapshot
Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks
inferred← citeshttps://doi.org/10.1038/s41467-019-14052-xopenalex-snapshot
Divergent mutational processes distinguish hypoxic and normoxic tumours
inferred← citeshttps://doi.org/10.1038/s41467-021-21081-yopenalex-snapshot
A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement
inferred← citeshttps://doi.org/10.1038/s41586-020-1969-6openalex-snapshot
Pan-cancer analysis of whole genomes
inferred← citeshttps://doi.org/10.1093/nar/gkz774openalex-snapshot
regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants
inferred← citeshttps://doi.org/10.1093/narcan/zcab001openalex-snapshot
Systematic identification of non-coding somatic single nucleotide variants associated with altered transcription and DNA methylation in adult and pediatric cancers
inferred← citeshttps://doi.org/10.1101/179705openalex-snapshot
Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours
inferred← citeshttps://doi.org/10.1101/190330openalex-snapshot
The whole-genome panorama of cancer drivers
inferred← citeshttps://doi.org/10.1101/2020.02.13.20017921openalex-snapshot
The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support
inferred← citeshttps://doi.org/10.1101/215244openalex-snapshot
DriverPower: Combined burden and functional impact tests for cancer driver discovery
inferred← citeshttps://doi.org/10.1101/225441openalex-snapshot
Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
inferred← citeshttps://doi.org/10.1101/237313openalex-snapshot
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
inferred← citeshttps://doi.org/10.1101/280446openalex-snapshot
Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences
inferred← citeshttps://doi.org/10.1101/623215openalex-snapshot
A Bayesian Nonparametric Approach to Discover Clinico-Genetic Associations across Cancer Types
inferred← citeshttps://doi.org/10.1186/s13059-019-1818-9openalex-snapshot
Global impact of somatic structural variation on the DNA methylome of human cancers
inferred← citeshttps://doi.org/10.2217/bmm-2020-0025openalex-snapshot
Predictive and Patient-Monitoring Biomarkers: Precision in the Management of Colorectal Cancer
inferred← citeshttps://doi.org/10.2217/pgs-2020-0011openalex-snapshot
Precision in Cancer Pharmacogenomics
inferred← citeshttps://doi.org/10.48550/arxiv.1904.12973openalex-snapshot
Unsupervised Extraction of Phenotypes from Cancer Clinical Notes for Association Studies
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