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Disruption of ubiquitin mediated proteolysis is a widespread mechanism of tumorigenesis

https://doi.org/10.1101/507764
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What this work says

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

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UCSF Chimera—A visualization system for exploratory research and analysis
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Ubiquitin-Mediated Proteolysis and Human Disease
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Prediction of Protein Secondary Structure
inferredcites →https://doi.org/10.1007/978-1-4939-6406-2_6openalex-snapshot
SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks
inferredcites →https://doi.org/10.1016/0022-2836(84)90309-7openalex-snapshot
Analysis of membrane and surface protein sequences with the hydrophobic moment plot
inferredcites →https://doi.org/10.1016/j.bbamcr.2013.02.028openalex-snapshot
The ubiquitin proteasome system — Implications for cell cycle control and the targeted treatment of cancer
inferredcites →https://doi.org/10.1016/j.bbcan.2017.12.004openalex-snapshot
Chaperoning the guardian of the genome. The two-faced role of molecular chaperones in p53 tumor suppressor action
inferredcites →https://doi.org/10.1016/j.bbrc.2006.09.163openalex-snapshot
Mutual regulation of conventional protein kinase C and a ubiquitin ligase complex
inferredcites →https://doi.org/10.1016/j.cell.2013.01.055openalex-snapshot
Competing E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm
inferredcites →https://doi.org/10.1016/j.cell.2016.03.014openalex-snapshot
On the Dependency of Cellular Protein Levels on mRNA Abundance
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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
inferredcites →https://doi.org/10.1016/j.cell.2017.09.042openalex-snapshot
Universal Patterns of Selection in Cancer and Somatic Tissues
inferredcites →https://doi.org/10.1016/j.cell.2018.02.060openalex-snapshot
Comprehensive Characterization of Cancer Driver Genes and Mutations
inferredcites →https://doi.org/10.1016/j.cell.2018.06.001openalex-snapshot
Universal Patterns of Selection in Cancer and Somatic Tissues
inferredcites →https://doi.org/10.1016/j.cell.2018.07.034openalex-snapshot
Comprehensive Characterization of Cancer Driver Genes and Mutations
inferredcites →https://doi.org/10.1016/j.cellsig.2016.02.009openalex-snapshot
Regulation of BRAF protein stability by a negative feedback loop involving the MEK–ERK pathway but not the FBXW7 tumour suppressor
inferredcites →https://doi.org/10.1016/j.celrep.2018.03.047openalex-snapshot
Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types
inferredcites →https://doi.org/10.1016/j.cels.2017.08.013openalex-snapshot
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer
inferredcites →https://doi.org/10.1016/j.cels.2018.03.002openalex-snapshot
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
inferredcites →https://doi.org/10.1016/j.dnarep.2010.09.011openalex-snapshot
The ubiquitous role of ubiquitin in the DNA damage response
inferredcites →https://doi.org/10.1016/j.jmb.2005.01.071openalex-snapshot
The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins
inferredcites →https://doi.org/10.1016/j.semcdb.2010.09.006openalex-snapshot
E3 ubiquitin ligases in ErbB receptor quantity control
inferredcites →https://doi.org/10.1016/s1097-2765(02)00519-1openalex-snapshot
The PHD Domain of MEKK1 Acts as an E3 Ubiquitin Ligase and Mediates Ubiquitination and Degradation of ERK1/2
inferredcites →https://doi.org/10.1021/pr501005vopenalex-snapshot
Proteomic Analysis and Identification of Cellular Interactors of the Giant Ubiquitin Ligase HERC2
inferredcites →https://doi.org/10.1038/cr.2016.35openalex-snapshot
E2 enzymes: more than just middle men
inferredcites →https://doi.org/10.1038/nature08011openalex-snapshot
F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage
inferredcites →https://doi.org/10.1038/nature11003openalex-snapshot
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
inferredcites →https://doi.org/10.1038/nature18003openalex-snapshot
Proteogenomics connects somatic mutations to signalling in breast cancer
inferredcites →https://doi.org/10.1038/ncomms10239openalex-snapshot
Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system
inferredcites →https://doi.org/10.1038/ncomms3741openalex-snapshot
From protein sequence to dynamics and disorder with DynaMine
inferredcites →https://doi.org/10.1038/ng.2892openalex-snapshot
A general framework for estimating the relative pathogenicity of human genetic variants
inferredcites →https://doi.org/10.1038/ng.3969openalex-snapshot
Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease
inferredcites →https://doi.org/10.1038/nmeth.2642openalex-snapshot
IntOGen-mutations identifies cancer drivers across tumor types
inferredcites →https://doi.org/10.1038/nmeth.2650openalex-snapshot
TCPA: a resource for cancer functional proteomics data
inferredcites →https://doi.org/10.1038/nmeth.3622openalex-snapshot
TransVar: a multilevel variant annotator for precision genomics
inferredcites →https://doi.org/10.1038/nrc1299openalex-snapshot
A census of human cancer genes
inferredcites →https://doi.org/10.1038/nrm2731openalex-snapshot
Breaking the chains: structure and function of the deubiquitinases
inferredcites →https://doi.org/10.1038/sj.emboj.7601120openalex-snapshot
Distinct functions of the ubiquitin–proteasome pathway influence nucleotide excision repair
inferredcites →https://doi.org/10.1038/srep02650openalex-snapshot
Comprehensive identification of mutational cancer driver genes across 12 tumor types
inferredcites →https://doi.org/10.1073/pnas.0806268105openalex-snapshot
Cancer related mutations in NRF2 impair its recognition by Keap1-Cul3 E3 ligase and promote malignancy
inferredcites →https://doi.org/10.1073/pnas.1215510110openalex-snapshot
Proteasome inhibition rescues clinically significant unstable variants of the mismatch repair protein Msh2
inferredcites →https://doi.org/10.1073/pnas.1608644113openalex-snapshot
Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination
inferredcites →https://doi.org/10.1073/pnas.77.3.1365openalex-snapshot
ATP-dependent conjugation of reticulocyte proteins with the polypeptide required for protein degradation.
inferredcites →https://doi.org/10.1073/pnas.77.4.1783openalex-snapshot
Proposed role of ATP in protein breakdown: conjugation of protein with multiple chains of the polypeptide of ATP-dependent proteolysis.
inferredcites →https://doi.org/10.1073/pnas.96.11.6273openalex-snapshot
β-Trcp couples β-catenin phosphorylation-degradation and regulates Xenopus axis formation
inferredcites →https://doi.org/10.1074/jbc.m703320200openalex-snapshot
Amplitude Control of Protein Kinase C by RINCK, a Novel E3 Ubiquitin Ligase
inferredcites →https://doi.org/10.1074/mcp.o111.014076openalex-snapshot
E3Net: A System for Exploring E3-mediated Regulatory Networks of Cellular Functions
inferredcites →https://doi.org/10.1093/bioinformatics/btm270openalex-snapshot
Predicting functionally important residues from sequence conservation
inferredcites →https://doi.org/10.1093/bioinformatics/btx812openalex-snapshot
TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data
inferredcites →https://doi.org/10.1093/nar/gkac1052openalex-snapshot
UniProt: the Universal Protein Knowledgebase in 2023
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gks1094openalex-snapshot
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
inferredcites →https://doi.org/10.1093/nar/gku1267openalex-snapshot
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
inferredcites →https://doi.org/10.1093/nar/gkv1291openalex-snapshot
ELM 2016—data update and new functionality of the eukaryotic linear motif resource
inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot
The Pfam protein families database: towards a more sustainable future
inferredcites →https://doi.org/10.1101/140475openalex-snapshot
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
inferredcites →https://doi.org/10.1101/gr.139758.112openalex-snapshot
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation
inferredcites →https://doi.org/10.1109/mcse.2007.53openalex-snapshot
IPython: A System for Interactive Scientific Computing
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1111/j.1399-3011.1988.tb01258.xopenalex-snapshot
Positional flexibilities of amino acid residues in globular proteins
inferredcites →https://doi.org/10.1126/scisignal.aak9982openalex-snapshot
Degrons in cancer
inferredcites →https://doi.org/10.1128/mcb.00050-07openalex-snapshot
Ubiquitination and Degradation of Mutant p53
inferredcites →https://doi.org/10.1158/0008-5472.can-07-0967openalex-snapshot
Differential Regulation of Estrogen Receptor α Turnover and Transactivation by Mdm2 and Stress-Inducing Agents
inferredcites →https://doi.org/10.1186/gb-2013-14-9-r106openalex-snapshot
The mutational landscape of chromatin regulatory factors across 4,623 tumor samples
inferredcites →https://doi.org/10.1186/s13059-016-0994-0openalex-snapshot
OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations
inferredcites →https://doi.org/10.1186/s13073-015-0260-1openalex-snapshot
Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types
inferredcites →https://doi.org/10.1186/s13073-018-0531-8openalex-snapshot
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
inferredcites →https://doi.org/10.1210/me.2007-0449openalex-snapshot
Estrogen Receptor-α Hinge-Region Lysines 302 and 303 Regulate Receptor Degradation by the Proteasome
inferredcites →https://doi.org/10.1371/journal.pcbi.1000376openalex-snapshot
Prediction of Protein Binding Regions in Disordered Proteins
inferredcites →https://doi.org/10.18632/oncotarget.8752openalex-snapshot
Altered oncomodules underlie chromatin regulatory factors driver mutations
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
inferredcites →https://doi.org/10.7490/f1000research.1095265.1openalex-snapshot
A general framework for estimating the relative pathogenicity of human genetic variants

What points at this work

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

inferred← citeshttps://doi.org/10.1002/path.6446openalex-snapshot
Analysis of IDH1 and IDH2 mutations as causes of the hypermethylator phenotype in colorectal cancer
inferred← citeshttps://doi.org/10.1101/2020.01.29.924860openalex-snapshot
The consequences of variant calling decisions in secondary analyses of cancer sequencing data
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