Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer

Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes

(2015) Jüri Reimand et al.   PLoS Genetics

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

(2014) Alvin Leung et al.   BIOINFORMATICS

SF3B1mutations constitute a novel therapeutic target in breast cancer

(2014) Sarah L Maguire et al.   JOURNAL OF PATHOLOGY

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

(2014) S. C. Mack et al.   NATURE

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

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A global assessment of cancer genomic alterations in epigenetic mechanisms

(2014) Muhammad A Shah et al.   Epigenetics & Chromatin

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas

(2013) Sebastian Bender et al.   CANCER CELL

Acetylation of p53 stimulates miRNA processing and determines cell survival following genotoxic stress

(2013) Jonathan Chang et al.   EMBO JOURNAL

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

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Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

(2013) Christoph Plass et al.   NATURE REVIEWS GENETICS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

The mutational landscape of phosphorylation signaling in cancer

(2013) Jüri Reimand et al.   Scientific Reports

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

(2013) Abel Gonzalez-Perez et al.   GENOME BIOLOGY

Domain-mediated protein interaction prediction: From genome to network

(2012) Jüri Reimand et al.   FEBS LETTERS

MuSiC: Identifying mutational significance in cancer genomes

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Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

(2012) Paul A. Northcott et al.   NATURE

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

(2012) Gang Wu et al.   NATURE GENETICS

UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation

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Hallmarks of Cancer: The Next Generation

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SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

(2011) E. Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

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SMART 7: recent updates to the protein domain annotation resource

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PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Histone onco-modifications

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The Common Feature of Leukemia-Associated IDH1 and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting α-Ketoglutarate to 2-Hydroxyglutarate

(2010) Patrick S. Ward et al.   CANCER CELL

The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome

(2010) E. J. Song et al.   GENES & DEVELOPMENT

Novel histone deacetylase inhibitors in clinical trials as anti-cancer agents

(2010) Jiahuai Tan et al.   Journal of Hematology & Oncology

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(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

CPLA 1.0: an integrated database of protein lysine acetylation

(2010) Zexian Liu et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Mutational Heterogeneity in Human Cancers: Origin and Consequences

(2009) Jesse J. Salk et al.   Annual Review of Pathology-Mechanisms of Disease

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Targeting the ubiquitin system in cancer therapy

(2009) Daniela Hoeller et al.   NATURE

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

CORUM: the comprehensive resource of mammalian protein complexes—2009

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Proteome-wide prediction of acetylation substrates

(2009) A. Basu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The E3 Ligase TRAF6 Regulates Akt Ubiquitination and Activation

(2009) W.-L. Yang et al.   SCIENCE

Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects

(2008) Maria Fousteri et al.   CELL RESEARCH

Atypical ubiquitin chains: new molecular signals. ‘Protein Modifications: Beyond the Usual Suspects’ Review Series

(2008) Fumiyo Ikeda et al.   EMBO REPORTS

The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression

(2008) E. Shema et al.   GENES & DEVELOPMENT

A role for ubiquitin in the spliceosome assembly pathway

(2008) Priya Bellare et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling

Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300

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