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OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine

https://doi.org/10.1101/638866
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What this work says

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

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Current Landscape of Immunotherapy in Breast Cancer
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Cell cycle control in breast cancer cells
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Targeting the Breast Cancer Kinome
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PharmGKB: A worldwide resource for pharmacogenomic information
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PharmGKB: The Pharmacogenomics Knowledge Base
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Breast cancer risk associated with gene expression and genotype polymorphisms of the folate-metabolizing MTHFR gene: a case-control study in a high altitude Ecuadorian mestizo population
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Incidence of the L858R and G719S mutations of the epidermal growth factor receptor oncogene in an Ecuadorian population with lung cancer
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In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities
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UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis
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A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers
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Defining a Cancer Dependency Map
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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
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Comprehensive Characterization of Cancer Driver Genes and Mutations
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Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
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Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
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Oncogenic Signaling Pathways in The Cancer Genome Atlas
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Pathogenic Germline Variants in 10,389 Adult Cancers
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The Proteomic Landscape of Triple-Negative Breast Cancer
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Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
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DNA repair and damage pathways in breast cancer development and therapy
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The Immune Landscape of Cancer
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RNA-Binding Proteins in Cancer: Old Players and New Actors
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The role of JAK/STAT signalling in the pathogenesis, prognosis and treatment of solid tumours
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Identification of a novel serum biomarker for pancreatic cancer, C4b-binding protein α-chain (C4BPA) by quantitative proteomic analysis using tandem mass tags
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CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network
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Pharmacogenetics: From Bench to Byte— An Update of Guidelines
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The landscape of somatic copy-number alteration across human cancers
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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
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Sequence analysis of mutations and translocations across breast cancer subtypes
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Mutational landscape and significance across 12 major cancer types
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Discovery and saturation analysis of cancer genes across 21 tumour types
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Pharmacogenomic agreement between two cancer cell line data sets
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Identification of essential genes for cancer immunotherapy
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A comprehensive transcriptional portrait of human cancer cell lines
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Towards a knowledge-based Human Protein Atlas
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Patterns and functional implications of rare germline variants across 12 cancer types
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The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies
inferredcites →https://doi.org/10.1038/ncomms15350openalex-snapshot
Correction: Corrigendum: The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies
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The Cancer Genome Atlas Pan-Cancer analysis project
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Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells
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Comparison of algorithms for the detection of cancer drivers at subgene resolution
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
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Practical implications of gene-expression-based assays for breast oncologists
inferredcites →https://doi.org/10.1038/nrm.2017.130openalex-snapshot
A brave new world of RNA-binding proteins
inferredcites →https://doi.org/10.1038/onc.2013.533openalex-snapshot
Hallmarks of alternative splicing in cancer
inferredcites →https://doi.org/10.1038/s41467-018-06916-5openalex-snapshot
Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration
inferredcites →https://doi.org/10.1038/s41523-017-0007-9openalex-snapshot
A functionally significant SNP in TP53 and breast cancer risk in African-American women
inferredcites →https://doi.org/10.1038/s41568-018-0060-1openalex-snapshot
The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers
inferredcites →https://doi.org/10.1038/s41596-018-0103-9openalex-snapshot
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
inferredcites →https://doi.org/10.1038/s41598-017-01314-1openalex-snapshot
RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer
inferredcites →https://doi.org/10.1038/s41598-018-32264-xopenalex-snapshot
Analysis of Racial/Ethnic Representation in Select Basic and Applied Cancer Research Studies
inferredcites →https://doi.org/10.1038/s41598-018-35149-1openalex-snapshot
Gene prioritization, communality analysis, networking and metabolic integrated pathway to better understand breast cancer pathogenesis
inferredcites →https://doi.org/10.1038/sigtrans.2016.42openalex-snapshot
The paradoxical functions of EGFR during breast cancer progression
inferredcites →https://doi.org/10.1038/srep02650openalex-snapshot
Comprehensive identification of mutational cancer driver genes across 12 tumor types
inferredcites →https://doi.org/10.1038/srep40070openalex-snapshot
Benzyl Isothiocyanate potentiates p53 signaling and antitumor effects against breast cancer through activation of p53-LKB1 and p73-LKB1 axes
inferredcites →https://doi.org/10.1038/srep46290openalex-snapshot
OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes
inferredcites →https://doi.org/10.1056/nejmoa1516767openalex-snapshot
Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation
inferredcites →https://doi.org/10.1073/pnas.0704723105openalex-snapshot
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells
inferredcites →https://doi.org/10.1074/mcp.m115.047928openalex-snapshot
Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation*
inferredcites →https://doi.org/10.1074/mcp.m500279-mcp200openalex-snapshot
A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics
inferredcites →https://doi.org/10.1089/thy.2010.1642openalex-snapshot
The Canadian Pharmacogenomics Network for Drug Safety: A Model for Safety Pharmacology
inferredcites →https://doi.org/10.1093/bioinformatics/btx743openalex-snapshot
The OncoPPi Portal: an integrative resource to explore and prioritize protein–protein interactions for cancer target discovery
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/gkn923openalex-snapshot
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
inferredcites →https://doi.org/10.1093/nar/gkq482openalex-snapshot
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
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/gkx1132openalex-snapshot
The Reactome Pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gky1133openalex-snapshot
Open Targets Platform: new developments and updates two years on
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.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1101/gr.199935.115openalex-snapshot
Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks
inferredcites →https://doi.org/10.1126/science.1075762openalex-snapshot
The Protein Kinase Complement of the Human Genome
inferredcites →https://doi.org/10.1126/science.1133427openalex-snapshot
The Consensus Coding Sequences of Human Breast and Colorectal Cancers
inferredcites →https://doi.org/10.1126/science.1260419openalex-snapshot
Tissue-based map of the human proteome
inferredcites →https://doi.org/10.1126/science.aan2507openalex-snapshot
A pathology atlas of the human cancer transcriptome
inferredcites →https://doi.org/10.1126/scisignal.2004088openalex-snapshot
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
inferredcites →https://doi.org/10.1155/2018/4809183openalex-snapshot
Precision Medicine for Breast Cancer: The Paths to Truly Individualized Diagnosis and Treatment
inferredcites →https://doi.org/10.1155/2018/7463832openalex-snapshot
Mutational Analysis of Oncogenic AKT1 Gene Associated with Breast Cancer Risk in the High Altitude Ecuadorian Mestizo Population
inferredcites →https://doi.org/10.1158/2159-8290.cd-12-0095openalex-snapshot
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
inferredcites →https://doi.org/10.1186/1471-2164-16-s7-s5openalex-snapshot
Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis
inferredcites →https://doi.org/10.1186/gb-2011-12-4-r41openalex-snapshot
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
inferredcites →https://doi.org/10.1186/gb-2014-15-1-r14openalex-snapshot
Dissecting the expression landscape of RNA-binding proteins in human cancers
inferredcites →https://doi.org/10.1186/s12920-017-0286-xopenalex-snapshot
Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis
inferredcites →https://doi.org/10.1186/s13059-018-1612-0openalex-snapshot
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens
inferredcites →https://doi.org/10.1186/s13073-018-0531-8openalex-snapshot
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
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Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes
inferredcites →https://doi.org/10.1371/journal.pgen.1006589openalex-snapshot
Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression
inferredcites →https://doi.org/10.18632/oncotarget.8196openalex-snapshot
Genomic landscape of DNA repair genes in cancer
inferredcites →https://doi.org/10.3322/caac.21492openalex-snapshot
Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries
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Molecular Actions of Thyroid Hormone on Breast Cancer Cell Migration and Invasion via Cortactin/N-WASP
inferredcites →https://doi.org/10.3390/cancers10110422openalex-snapshot
Targeting the Hippo Pathway for Breast Cancer Therapy
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The Potential of Wnt Signaling Pathway in Cancer: A Focus on Breast Cancer

What points at this work

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

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Pharmacogenomics, biomarker network, and allele frequencies in colorectal cancer
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The close interaction between hypoxia-related proteins and metastasis in pancarcinomas
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Unraveling druggable cancer-driving proteins and targeted drugs using artificial intelligence and multi-omics analyses
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In silico analyses reveal new putative Breast Cancer RNA-binding proteins
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Metastatic signaling of hypoxia-related genes across TCGA Pan-Cancer types
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1727541/v1openalex-snapshot
RAC1: Comprehensive Analysis of Genetic Alteration, Prognostic and Immunological Role Over Tumor Profiles
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3365091/v1openalex-snapshot
Whole exome sequencing identifies novel variants of PIK3CA and validation of hotspot mutation by droplet digital PCR in Breast cancer among Indian Population.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-808746/v1openalex-snapshot
Single-nucleus lung transcriptomics and inflammatory responses in lethal COVID-19 reveal potential drugs in advanced-stage clinical trials
inferred← citeshttps://doi.org/10.26434/chemrxiv.12408074openalex-snapshot
In Silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19
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TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes
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