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

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What this work says

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

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Nuclear division cycle 80 promotes malignant progression and predicts clinical outcome in colorectal cancer

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Structural requirements of chromokinesin Kif4A for its proper function in mitosis

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Phosphatase: PP2A structural importance, regulation and its aberrant expression in cancer

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Epigenetics in Alternative Pre-mRNA Splicing

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Hallmarks of Cancer: The Next Generation

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Interactome Networks and Human Disease

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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

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Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

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Transcriptional Addiction in Cancer

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Conserved Tetramer Junction in the Kinetochore Ndc80 Complex

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Impact of Alternative Splicing on the Human Proteome

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The Functional Impact of Alternative Splicing in Cancer

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Nonsense-mediated mRNA Decay and Cancer

inferredcites →https://doi.org/10.1016/j.gene.2004.10.022openalex-snapshot

Function of alternative splicing

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Function of alternative splicing

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The Tolerance of a Modular Protein to Duplication and Deletion of Internal Repeats

inferredcites →https://doi.org/10.1016/j.jmb.2016.04.017openalex-snapshot

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

inferredcites →https://doi.org/10.1016/j.molcel.2012.05.037openalex-snapshot

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

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Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

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Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46

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Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

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Analyzing the First Drafts of the Human Proteome

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Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

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Gene Ontology: tool for the unification of biology

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RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E)

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Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

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Near-optimal probabilistic RNA-seq quantification

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Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

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Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer

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Spliced MDM2 isoforms promote mutant p53 accumulation and gain-of-function in tumorigenesis

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Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

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The Genotype-Tissue Expression (GTEx) project

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The Cancer Genome Atlas Pan-Cancer analysis project

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Identification of common genetic variants controlling transcript isoform variation in human whole blood

inferredcites →https://doi.org/10.1038/nmeth.2714openalex-snapshot

Assessment of transcript reconstruction methods for RNA-seq

inferredcites →https://doi.org/10.1038/nrc.2016.51openalex-snapshot

RNA splicing factors as oncoproteins and tumour suppressors

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Ubiquitin ligases in oncogenic transformation and cancer therapy

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Targeting RAS–ERK signalling in cancer: promises and challenges

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The deubiquitination enzyme USP46 functions as a tumor suppressor by controlling PHLPP-dependent attenuation of Akt signaling in colon cancer

inferredcites →https://doi.org/10.1038/onc.2013.533openalex-snapshot

Hallmarks of alternative splicing in cancer

inferredcites →https://doi.org/10.1038/onc.2015.318openalex-snapshot

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

inferredcites →https://doi.org/10.1038/s41389-019-0136-0openalex-snapshot

ESCRT-III is necessary for the integrity of the nuclear envelope in micronuclei but is aberrant at ruptured micronuclear envelopes generating damage

inferredcites →https://doi.org/10.1038/s41467-020-14367-0openalex-snapshot

Pathway and network analysis of more than 2500 whole cancer genomes

inferredcites →https://doi.org/10.1038/s41586-020-1965-xopenalex-snapshot

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

inferredcites →https://doi.org/10.1038/s41586-020-1969-6openalex-snapshot

Pan-cancer analysis of whole genomes

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Genomic basis for RNA alterations in cancer

inferredcites →https://doi.org/10.1038/sj.onc.1210243openalex-snapshot

Cell-specific responses to loss of cyclin-dependent kinases

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Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein

inferredcites →https://doi.org/10.1074/jbc.m111.233304openalex-snapshot

Cell-surface Receptor for Complement Component C1q (gC1qR) Is a Key Regulator for Lamellipodia Formation and Cancer Metastasis

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Tumor Necrosis Factor α-induced Desumoylation and Cytoplasmic Translocation of Homeodomain-interacting Protein Kinase 1 Are Critical for Apoptosis Signal-regulating Kinase 1-JNK/p38 Activation

inferredcites →https://doi.org/10.1074/jbc.m801014200openalex-snapshot

Differential Isoform Expression and Interaction with the P32 Regulatory Protein Controls the Subcellular Localization of the Splicing Factor U2AF26

inferredcites →https://doi.org/10.1074/mcp.m113.029413openalex-snapshot

Interactome Analysis Reveals that C1QBP (complement component 1, q subcomponent binding protein) Is Associated with Cancer Cell Chemotaxis and Metastasis

inferredcites →https://doi.org/10.1080/15384101.2016.1152430openalex-snapshot

Targeting NEK2 as a promising therapeutic approach for cancer treatment

inferredcites →https://doi.org/10.1080/23723556.2015.1085120openalex-snapshot

Mitochondrial respiratory defects promote the Warburg effect and cancer progression

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Xwalk: computing and visualizing distances in cross-linking experiments

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The Pfam Protein Families Database

inferredcites →https://doi.org/10.1093/nar/30.1.38openalex-snapshot

The Ensembl genome database project

inferredcites →https://doi.org/10.1093/nar/gki037openalex-snapshot

3did: interacting protein domains of known three-dimensional structure

inferredcites →https://doi.org/10.1093/nar/gkl971openalex-snapshot

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

inferredcites →https://doi.org/10.1093/nar/gkm1054openalex-snapshot

Alternative splicing and protein structure evolution

inferredcites →https://doi.org/10.1093/nar/gkr1065openalex-snapshot

The Pfam protein families database

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/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/gku1392openalex-snapshot

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

inferredcites →https://doi.org/10.1093/nar/gku340openalex-snapshot

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

inferredcites →https://doi.org/10.1093/nar/gkv210openalex-snapshot

Identification of recurrent regulated alternative splicing events across human solid tumors

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/10.1101/385294openalex-snapshot

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

inferredcites →https://doi.org/10.1101/cshperspect.a001107openalex-snapshot

Mutant p53 Gain-of-Function in Cancer

inferredcites →https://doi.org/10.1101/gad.261792.115openalex-snapshot

Structure of human MDM2 complexed with RPL11 reveals the molecular basis of p53 activation

inferredcites →https://doi.org/10.1111/1755-0998.12670openalex-snapshot

Detecting alternatively spliced transcript isoforms from single‐molecule long‐read sequences without a reference genome

inferredcites →https://doi.org/10.1111/cge.13089openalex-snapshot

NDUFA9 point mutations cause a variable mitochondrial complex I assembly defect

inferredcites →https://doi.org/10.1126/science.1221483openalex-snapshot

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

inferredcites →https://doi.org/10.1126/science.aad7297openalex-snapshot

Nuclear envelope rupture and repair during cancer cell migration

inferredcites →https://doi.org/10.1155/2015/862461openalex-snapshot

Role of NEK2A in Human Cancer and Its Therapeutic Potentials

inferredcites →https://doi.org/10.1158/0008-5472.can-13-2543openalex-snapshot

NF-κB Gene Signature Predicts Prostate Cancer Progression

inferredcites →https://doi.org/10.1158/1541-7786.mcr-16-0459openalex-snapshot

The Landscape of Isoform Switches in Human Cancers

inferredcites →https://doi.org/10.1172/jci64264openalex-snapshot

Mitochondrial complex I activity and NAD+/NADH balance regulate breast cancer progression

inferredcites →https://doi.org/10.1177/1947601912473306openalex-snapshot

Mitotic Stress and Chromosomal Instability in Cancer: The Case for TPX2

inferredcites →https://doi.org/10.1182/blood-2006-07-038232openalex-snapshot

Human RPS19, the gene mutated in Diamond-Blackfan anemia, encodes a ribosomal protein required for the maturation of 40S ribosomal subunits

inferredcites →https://doi.org/10.1186/gb-2013-14-7-r70openalex-snapshot

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

inferredcites →https://doi.org/10.1186/s12864-017-3899-8openalex-snapshot

Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans

inferredcites →https://doi.org/10.1186/s12864-017-4002-1openalex-snapshot

Evaluation and comparison of computational tools for RNA-seq isoform quantification

inferredcites →https://doi.org/10.1186/s12864-018-4869-5openalex-snapshot

Limitations of alignment-free tools in total RNA-seq quantification

inferredcites →https://doi.org/10.1242/dmm.031146openalex-snapshot

Homeodomain-interacting protein kinase promotes tumorigenesis and metastatic cell behavior

inferredcites →https://doi.org/10.1371/journal.pcbi.1005761openalex-snapshot

Stochastic principles governing alternative splicing of RNA

inferredcites →https://doi.org/10.1530/rep-12-0050openalex-snapshot

NPPC/NPR2 signaling is essential for oocyte meiotic arrest and cumulus oophorus formation during follicular development in the mouse ovary

inferredcites →https://doi.org/10.1593/neo.101744openalex-snapshot

Identification of an Exon 4-Deletion Variant of Epidermal Growth Factor Receptor with Increased Metastasis-Promoting Capacity

inferredcites →https://doi.org/10.3389/fgene.2015.00260openalex-snapshot

Correcting for the study bias associated with protein–protein interaction measurements reveals differences between protein degree distributions from different cancer types

inferredcites →https://doi.org/10.3389/fonc.2018.00408openalex-snapshot

The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism

inferredcites →https://doi.org/10.3390/ijms18071434openalex-snapshot

An Emerging Role for Tubulin Isotypes in Modulating Cancer Biology and Chemotherapy Resistance

inferredcites →https://doi.org/10.3390/jcm8040513openalex-snapshot

Systematic Multiomics Analysis of Alterations in C1QBP mRNA Expression and Relevance for Clinical Outcomes in Cancers

inferredcites →https://doi.org/10.3748/wjg.v23.i20.3675openalex-snapshot

Effect of NDC80 in human hepatocellular carcinoma

inferredcites →https://doi.org/10.3892/ijo.2016.3387openalex-snapshot

Role of ribosomal protein mutations in tumor development (Review)

inferredcites →https://doi.org/10.4103/1008-682x.127825openalex-snapshot

The role of mRNA splicing in prostate cancer

inferredcites →https://doi.org/10.7717/peerj.732openalex-snapshot

Tandem-repeat protein domains across the tree of life

What points at this work

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

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/s41467-020-14367-0openalex-snapshot

Pathway and network analysis of more than 2500 whole cancer genomes

inferred← citeshttps://doi.org/10.37349/ei.2023.00122openalex-snapshot

The role of complement component C1q in angiogenesis

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