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Pathway and network analysis of more than 2,500 whole cancer genomes

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What this work says

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

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The Catalogue of Somatic Mutations in Cancer (COSMIC)

inferredcites →https://doi.org/10.1016/j.cell.2011.02.013openalex-snapshot

Hallmarks of Cancer: The Next Generation

inferredcites →https://doi.org/10.1016/j.cell.2013.03.002openalex-snapshot

Lessons from the Cancer Genome

inferredcites →https://doi.org/10.1016/j.celrep.2018.01.088openalex-snapshot

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

inferredcites →https://doi.org/10.1016/j.leukres.2016.07.002openalex-snapshot

TLE4 regulation of wnt-mediated inflammation underlies its role as a tumor suppressor in myeloid leukemia

inferredcites →https://doi.org/10.1038/75556openalex-snapshot

Gene Ontology: tool for the unification of biology

inferredcites →https://doi.org/10.1038/nature08987openalex-snapshot

International network of cancer genome projects

inferredcites →https://doi.org/10.1038/nature12213openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature12912openalex-snapshot

Discovery and saturation analysis of cancer genes across 21 tumour types

inferredcites →https://doi.org/10.1038/ng.3141openalex-snapshot

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

inferredcites →https://doi.org/10.1038/ng.3168openalex-snapshot

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

inferredcites →https://doi.org/10.1038/nmeth.2562openalex-snapshot

Computational approaches to identify functional genetic variants in cancer genomes

inferredcites →https://doi.org/10.1038/nmeth.3440openalex-snapshot

Pathway and network analysis of cancer genomes

inferredcites →https://doi.org/10.1038/nmeth.4514openalex-snapshot

NetSig: network-based discovery from cancer genomes

inferredcites →https://doi.org/10.1038/nrc3638openalex-snapshot

The ID proteins: master regulators of cancer stem cells and tumour aggressiveness

inferredcites →https://doi.org/10.1038/srep02651openalex-snapshot

The mutational landscape of phosphorylation signaling in cancer

inferredcites →https://doi.org/10.1038/srep36257openalex-snapshot

SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis

inferredcites →https://doi.org/10.1073/pnas.1410419111openalex-snapshot

ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers

inferredcites →https://doi.org/10.1089/cmb.2010.0265openalex-snapshot

Algorithms for Detecting Significantly Mutated Pathways in Cancer

inferredcites →https://doi.org/10.1089/dna.2013.2201openalex-snapshot

TP53 Promoter Methylation in Primary Glioblastoma: Relationship with TP53 mRNA and Protein Expression and Mutation Status

inferredcites →https://doi.org/10.1093/bioinformatics/btt471openalex-snapshot

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

inferredcites →https://doi.org/10.1093/bioinformatics/bty613openalex-snapshot

Hierarchical HotNet: identifying hierarchies of altered subnetworks

inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/gkj109openalex-snapshot

BioGRID: a general repository for interaction datasets

inferredcites →https://doi.org/10.1093/nar/gkm936openalex-snapshot

CORUM: the comprehensive resource of mammalian protein complexes

inferredcites →https://doi.org/10.1093/nar/gkn653openalex-snapshot

PID: The Pathway Interaction Database

inferredcites →https://doi.org/10.1093/nar/gkp914openalex-snapshot

CORUM: the comprehensive resource of mammalian protein complexes—2009

inferredcites →https://doi.org/10.1093/nar/gkq1018openalex-snapshot

Reactome: a database of reactions, pathways and biological processes

inferredcites →https://doi.org/10.1093/nar/gkq1200openalex-snapshot

DIMA 3.0: Domain Interaction Map

inferredcites →https://doi.org/10.1093/nar/gkt1102openalex-snapshot

The Reactome pathway knowledgebase

inferredcites →https://doi.org/10.1093/nar/gkt887openalex-snapshot

3did: a catalog of domain-based interactions of known three-dimensional structure

inferredcites →https://doi.org/10.1093/nar/gku1003openalex-snapshot

STRING v10: protein–protein interaction networks, integrated over the tree of life

inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot

The Reactome pathway Knowledgebase

inferredcites →https://doi.org/10.1093/nar/gkw1102openalex-snapshot

The BioGRID interaction database: 2017 update

inferredcites →https://doi.org/10.1093/nar/gkw1107openalex-snapshot

InterPro in 2017—beyond protein family and domain annotations

inferredcites →https://doi.org/10.1093/nar/gkw1108openalex-snapshot

Expansion of the Gene Ontology knowledgebase and resources

inferredcites →https://doi.org/10.1093/nar/gkw199openalex-snapshot

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

inferredcites →https://doi.org/10.1101/237313openalex-snapshot

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

inferredcites →https://doi.org/10.1101/322859openalex-snapshot

The Repertoire of Mutational Signatures in Human Cancer

inferredcites →https://doi.org/10.1101/cshperspect.a007906openalex-snapshot

TCF/LEFs and Wnt Signaling in the Nucleus

inferredcites →https://doi.org/10.1101/gad.12.13.1931openalex-snapshot

Groucho proteins: transcriptional corepressors for specific subsets of DNA-binding transcription factors in vertebrates and invertebrates

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

inferredcites →https://doi.org/10.1126/science.1235122openalex-snapshot

Cancer Genome Landscapes

inferredcites →https://doi.org/10.1182/blood-2007-07-103291openalex-snapshot

Loss of TLE1 and TLE4 from the del(9q) commonly deleted region in AML cooperates with AML1-ETO to affect myeloid cell proliferation and survival

inferredcites →https://doi.org/10.1186/1471-2105-9-405openalex-snapshot

iRefIndex: A consolidated protein interaction database with provenance

inferredcites →https://doi.org/10.1371/journal.pgen.1006773openalex-snapshot

Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature

inferredcites →https://doi.org/10.1371/journal.pone.0133503openalex-snapshot

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration

inferredcites →https://doi.org/10.18632/oncotarget.11930openalex-snapshot

Molecular alterations and tumor suppressive function of the DUSP22 (Dual Specificity Phosphatase 22) gene in peripheral T-cell lymphoma subtypes

What points at this work

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

inferred← citeshttps://doi.org/10.1002/eji.202048712openalex-snapshot

Critical cancer vulnerabilities identified by unbiased CRISPR/Cas9 screens inform on efficient cancer Immunotherapy

inferred← citeshttps://doi.org/10.1002/med.21741openalex-snapshot

RNA splicing alteration in the response to platinum chemotherapy in ovarian cancer: A possible biomarker and therapeutic target

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.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/s41380-025-03118-6openalex-snapshot

Gene expression signatures of response to fluoxetine treatment: systematic review and meta-analyses

inferred← citeshttps://doi.org/10.1038/s41467-019-13983-9openalex-snapshot

Integrative pathway enrichment analysis of multivariate omics data

inferred← citeshttps://doi.org/10.1038/s41568-022-00502-0openalex-snapshot

Big data in basic and translational cancer research

inferred← citeshttps://doi.org/10.1038/s41596-018-0103-9openalex-snapshot

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

inferred← citeshttps://doi.org/10.1038/s41598-020-71221-5openalex-snapshot

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

inferred← citeshttps://doi.org/10.1038/s42004-024-01103-8openalex-snapshot

All paths lead to hubs in the spectroscopic networks of water isotopologues H216O and H218O

inferred← citeshttps://doi.org/10.1038/s43018-021-00250-4openalex-snapshot

Moving pan-cancer studies from basic research toward the clinic

inferred← citeshttps://doi.org/10.1093/bioinformatics/btae257openalex-snapshot

Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks

inferred← citeshttps://doi.org/10.1093/nar/gkz451openalex-snapshot

IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations

inferred← citeshttps://doi.org/10.1101/2021.06.29.450342openalex-snapshot

Discovering cancer driver genes and pathways using stochastic block model graph neural networks

inferred← citeshttps://doi.org/10.1101/2024.08.13.607019openalex-snapshot

Enzyme family-centred approach identifies helicases as recurrent hemizygous tumour suppressor genes

inferred← citeshttps://doi.org/10.1101/214494openalex-snapshot

A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations

inferred← citeshttps://doi.org/10.1101/742379openalex-snapshot

Pathogenic impact of transcript isoform switching in 1209 cancer samples covering 27 cancer types using an isoform-specific interaction network

inferred← citeshttps://doi.org/10.30574/wjbphs.2024.17.2.0046openalex-snapshot

Reviewing the progress of cancer research in the USA

inferred← citeshttps://doi.org/10.3389/fcell.2019.00079openalex-snapshot

The Good, the Bad and the Tick

inferred← citeshttps://doi.org/10.3390/jpm13111590openalex-snapshot

Systems Biology in Cancer Diagnosis Integrating Omics Technologies and Artificial Intelligence to Support Physician Decision Making

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