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Genome-wide analysis of p53-regulated transcription in Myc-driven lymphomas

https://doi.org/10.1038/onc.2016.443

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Bcl-2 Mediates Chemoresistance in Matched Pairs of Primary Eμ-myc Lymphomas in Vivo

inferredcites →https://doi.org/10.1016/j.ccr.2006.10.010openalex-snapshot

Mdm2 is critically and continuously required to suppress lethal p53 activity in vivo

inferredcites →https://doi.org/10.1016/j.ccr.2010.08.007openalex-snapshot

An ARF-Independent c-MYC-Activated Tumor Suppression Pathway Mediated by Ribosomal Protein-Mdm2 Interaction

inferredcites →https://doi.org/10.1016/j.cell.2005.10.043openalex-snapshot

A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

inferredcites →https://doi.org/10.1016/j.cell.2006.12.007openalex-snapshot

Modeling the Therapeutic Efficacy of p53 Restoration in Tumors

inferredcites →https://doi.org/10.1016/j.cell.2009.04.037openalex-snapshot

Blinded by the Light: The Growing Complexity of p53

inferredcites →https://doi.org/10.1016/j.celrep.2014.06.030openalex-snapshot

A Comprehensive and High-Resolution Genome-wide Response of p53 to Stress

inferredcites →https://doi.org/10.1016/j.molcel.2012.01.020openalex-snapshot

Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells

inferredcites →https://doi.org/10.1016/s0092-8674(00)80452-3openalex-snapshot

Tumor Suppression at the Mouse INK4a Locus Mediated by the Alternative Reading Frame Product p19

inferredcites →https://doi.org/10.1016/s1097-2765(01)00284-2openalex-snapshot

p53DINP1, a p53-Inducible Gene, Regulates p53-Dependent Apoptosis

inferredcites →https://doi.org/10.1038/318533a0openalex-snapshot

The c-myc oncogene driven by immunoglobulin enhancers induces lymphoid malignancy in transgenic mice

inferredcites →https://doi.org/10.1038/79542openalex-snapshot

Genetic analysis of chemoresistance in primary murine lymphomas

inferredcites →https://doi.org/10.1038/cdd.2012.89openalex-snapshot

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis

inferredcites →https://doi.org/10.1038/nature05529openalex-snapshot

Senescence and tumour clearance is triggered by p53 restoration in murine liver carcinomas

inferredcites →https://doi.org/10.1038/nature05541openalex-snapshot

Restoration of p53 function leads to tumour regression in vivo

inferredcites →https://doi.org/10.1038/nature13537openalex-snapshot

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

inferredcites →https://doi.org/10.1038/ng1180openalex-snapshot

PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

inferredcites →https://doi.org/10.1038/ng1572openalex-snapshot

Temporal dissection of p53 function in vitro and in vivo

inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot

Mapping and quantifying mammalian transcriptomes by RNA-Seq

inferredcites →https://doi.org/10.1038/nmeth890openalex-snapshot

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

inferredcites →https://doi.org/10.1038/nprot.2008.211openalex-snapshot

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

inferredcites →https://doi.org/10.1038/nrc3711openalex-snapshot

Unravelling mechanisms of p53-mediated tumour suppression

inferredcites →https://doi.org/10.1038/nrm2395openalex-snapshot

Transcriptional control of human p53-regulated genes

inferredcites →https://doi.org/10.1038/onc.2011.35openalex-snapshot

The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor

inferredcites →https://doi.org/10.1073/pnas.0506580102openalex-snapshot

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btr064openalex-snapshot

FIMO: scanning for occurrences of a given motif

inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkn923openalex-snapshot

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

inferredcites →https://doi.org/10.1093/nar/gkt504openalex-snapshot

Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells

inferredcites →https://doi.org/10.1093/nar/gkt997openalex-snapshot

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

inferredcites →https://doi.org/10.1101/gad.13.20.2658openalex-snapshot

Disruption of the ARF-Mdm2-p53 tumor suppressor pathway in Myc-induced lymphomagenesis

inferredcites →https://doi.org/10.1101/gad.13.20.2670openalex-snapshot

INK4a/ARF mutations accelerate lymphomagenesis and promote chemoresistance by disabling p53

inferredcites →https://doi.org/10.1101/gad.212282.112openalex-snapshot

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses

inferredcites →https://doi.org/10.1101/gr.133280.111openalex-snapshot

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

inferredcites →https://doi.org/10.1101/gr.181883.114openalex-snapshot

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity

inferredcites →https://doi.org/10.1126/science.1092472openalex-snapshot

In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2

inferredcites →https://doi.org/10.1172/jci44504openalex-snapshot

Restoring expression of wild-type p53 suppresses tumor growth but does not cause tumor regression in mice with a p53 missense mutation

inferredcites →https://doi.org/10.1186/1747-1028-7-6openalex-snapshot

Two sides of the Myc-induced DNA damage response: from tumor suppression to tumor maintenance

inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot

Bioconductor: open software development for computational biology and bioinformatics

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1371/journal.pgen.1003726openalex-snapshot

Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53's Tumor Suppressor Functions

inferredcites →https://doi.org/10.1371/journal.pgen.1004885openalex-snapshot

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation

inferredcites →https://doi.org/10.1371/journal.pone.0017574openalex-snapshot

Role of p53 Serine 46 in p53 Target Gene Regulation

inferredcites →https://doi.org/10.18632/oncotarget.5232openalex-snapshot

Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Gene Co-Expression Networks Describe the Catalytic Inhibition of DNA Topoisomerase Iigene

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Resistance to endocrine therapy in HR + and/or HER2 + breast cancer: the most promising predictive biomarkers

inferred← citeshttps://doi.org/10.1016/j.isci.2019.04.006openalex-snapshot

Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the Genome

inferred← citeshttps://doi.org/10.1016/j.molcel.2017.07.028openalex-snapshot

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

inferred← citeshttps://doi.org/10.1016/j.psj.2022.102164openalex-snapshot

Characterization of chicken p53 transcriptional function via parallel genome-wide chromatin occupancy and gene expression analysis

inferred← citeshttps://doi.org/10.1038/cdd.2017.174openalex-snapshot

Mechanisms of transcriptional regulation by p53

inferred← citeshttps://doi.org/10.1038/s41523-023-00582-7openalex-snapshot

Multidimensional quantitative phenotypic and molecular analysis reveals neomorphic behaviors of p53 missense mutants

inferred← citeshttps://doi.org/10.1073/pnas.2025539118openalex-snapshot

The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs

inferred← citeshttps://doi.org/10.1093/nar/gkaa666openalex-snapshot

Tumor suppressor p53: from engaging DNA to target gene regulation

inferred← citeshttps://doi.org/10.1101/gr.220533.117openalex-snapshot

Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity

inferred← citeshttps://doi.org/10.15252/embj.2020105464openalex-snapshot

Integrated requirement of non‐specific and sequence‐specific DNA binding in Myc‐driven transcription

inferred← citeshttps://doi.org/10.7150/jca.26502openalex-snapshot

Spontaneous Cancers, But Not Many Induced Ones in Animals, Resemble Semi-New Organisms that Possess a Unique Programmed Cell Death Mode Different from Apoptosis, Senescent Death, Necrosis and Stress-Induced Cell Death

inferred← citeshttps://doi.org/10.7150/jca.41324openalex-snapshot

Evidence for immortality and autonomy in animal cancer models is often not provided, which causes confusion on key issues of cancer biology

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