gene

RNA

Entity Detail — Knowledge Graph Node

Understanding Entity Pages

This page aggregates everything SciDEX knows about RNA: its mechanistic relationships (Knowledge Graph edges), hypotheses targeting it, analyses mentioning it, and supporting scientific papers. The interactive graph below shows its immediate neighbors. All content is AI-synthesized from peer-reviewed literature.

5215Connections
30Hypotheses
16Analyses
50Outgoing
50Incoming
1Experiments
20Debates

Summary

Page for RNA Binding Fox-1 Homolog 2 (RBFOX2)

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🧬 Gene Info
Gene SymbolRNA
AliasesRBFOX2, RBFOX3, RBFOX1
Chromosome22q12.3
Primary Expressionhippocampus, spinal cord, cortex, cerebellum, prefrontal cortex
Pathwaysunfolded protein response, ferroptosis, PI3K-AKT-mTOR signaling, ubiquitin-proteasome, apoptosis pathway
GeneCardsRNA
Human Protein AtlasRNA
Associated Diseasesaging, Als, Alzheimer, Alzheimer's disease
Known Drugs/Compoundsdimethyl fumarate, ketamine, lecanemab, levodopa, quercetin, rapamycin
InteractionsABCA7, ABCB1, ACLY, ACTB, Actin, ACVR2A
SciDEX HypothesesCell-state stratification is required to resolve m
Perturbation-first validation should precede thera
Advancing Beyond Traditional Druggability Through (+1 more)
KG Connections5213 knowledge graph edges
DatabasesGeneCardsUniProtNCBI GeneHPASTRING

Wiki Pages (21)

Knowledge base pages for this entity

Canonical Page

RNA Therapeutics for Neurodegeneration Investment Landscape

investment · 3955 words

RNA Metabolism Dysregulation in Alzheimer's Disease

mechanism · 4024 words

Validated Hypothesis: Gamma Oscillation Entrainment Enhances lncRNA-9969-Mediated Autophagy Through PV Interneuron-Specific ceRNA Networks

hypothesis · 3897 words

RNA-Targeted Therapies in Neurodegeneration

mechanism · 3272 words

ALS RNA Metabolism and Proteostasis Failure

mechanism · 3179 words

RNASEK — Ribonuclease Kappa

gene · 3161 words

Pathway Diagram

graph TD
    subgraph Pathology["Pathology"]
        RNA["RNA"] -->|"associated with"| astrocytes["astrocytes"]
    end
    subgraph Signaling["Signaling"]
        RNA["RNA"] -->|"activates"| microglia["microglia"]
        RNA["RNA"] -->|"activates"| SQSTM1["SQSTM1"]
        RNA["RNA"] -->|"activates"| neurodegeneration["neurodegeneration"]
        RNA["RNA"] -->|"regulates"| neurodegeneration_1["neurodegeneration"]
        m6A_Modification["m6A Modification"] -->|"modulates"| RNA["RNA"]
        BECN1["BECN1"] -->|"activates"| RNA["RNA"]
        rapamycin["rapamycin"] -->|"activates"| RNA["RNA"]
        rapamycin_3["rapamycin"] -->|"regulates"| RNA["RNA"]
        Stress_Granules["Stress Granules"] -->|"regulates"| RNA["RNA"]
    end
    subgraph Therapeutic["Therapeutic"]
        RNA["RNA"] -->|"expressed in"| hippocampus["hippocampus"]
        RNA["RNA"] -->|"expressed in"| spinal_cord["spinal cord"]
        rapamycin_4["rapamycin"] -->|"targets"| RNA["RNA"]
    end
    subgraph Interactions["Interactions"]
        RNA["RNA"] -->|"participates in"| unfolded_protein_response["unfolded protein response"]
        RNA["RNA"] -->|"interacts with"| neurodegeneration_2["neurodegeneration"]
    end
    style RNA fill:#4a1a6b,stroke:#4fc3f7,stroke-width:3px,color:#e0e0e0,font-weight:bold
    style astrocytes fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style microglia fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style hippocampus fill:#90a4ae,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style unfolded_protein_response fill:#1b5e20,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style SQSTM1 fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style neurodegeneration fill:#ef5350,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style neurodegeneration_1 fill:#ef5350,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style spinal_cord fill:#90a4ae,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style neurodegeneration_2 fill:#ef5350,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style m6A_Modification fill:#1b5e20,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style BECN1 fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style rapamycin fill:#90a4ae,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style rapamycin_3 fill:#90a4ae,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style rapamycin_4 fill:#1b5e20,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style Stress_Granules fill:#1b5e20,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0

Outgoing (2988)

TargetRelationTypeStr
neuronsregulatescell_type0.90
frontotemporal dementiainteracts_withdisease0.90
PI3K-AKT-mTOR signalingparticipates_inpathway0.90
T cellsexpressed_incell_type0.90
Alzheimer's diseaseregulatesdisease0.90

Incoming (2227)

SourceRelationTypeStr
rapamycintargetsdrug0.90
DNAassociated_withgene0.90
SETXbindsprotein0.90
BECN1activatesgene0.90
Stress Granulesregulatesprocess0.90

Targeting Hypotheses (30)

Hypotheses where this entity is a therapeutic target

HypothesisScoreDiseaseAnalysis
RBM45 Liquid-Liquid Phase Separation Dominance Hijacks RNA P 0.868 als -
Gamma Oscillation Entrainment Enhances lncRNA-9969-Mediated 0.865 molecular-neurobiology How does lncRNA-0021 achieve sequence-sp
SFPQ Paralog Displacement Triggers Cryptic Polyadenylation a 0.864 als -
hnRNP A2/B1 Staufen2-Mediated Axonal RNA Granule Transport F 0.851 als -
TDP-43 RNA-proteostasis failure across ALS, FTD, and AD/LATE 0.828 multi Cross-disease neurodegeneration mechanis
GLE1-Mediated mRNA Export Defect Creates Translation-Compete 0.823 als -
Calcium-Dysregulated mPTP Opening as an Alternative mtDNA Re 0.804 neurodegeneration What are the mechanisms by which gut mic
MATR3 Nuclear Body Disruption Impairs RNA Processing Hubs an 0.801 als -
Stress-granule RNA-binding protein phase transition across A 0.780 multi Cross-disease neurodegeneration mechanis
METTL3-Mediated m6A Modification of lncRNA-0021 Regulates mi 0.769 molecular-neurobiology How does lncRNA-0021 achieve sequence-sp
Seed-Proximal Asymmetric Duplex Stability Confers lncRNA-002 0.733 molecular-neurobiology How does lncRNA-0021 achieve sequence-sp
m6A RNA Modification as Address Code for Granule Targeting 0.700 neurodegeneration What determines the specificity of RNA-p
C9orf72 repeat RNA and dipeptide-repeat toxicity in ALS/FTD 0.700 neurodegeneration Test
Axonal RNA Transport Reconstitution 0.695 neurodegeneration RNA binding protein dysregulation across
hnRNPA2B1-Mediated Structural Remodeling Controls lncRNA-002 0.684 molecular-neurobiology How does lncRNA-0021 achieve sequence-sp
FUS Phase Separation Dominance in FTD-TDP: Aberrant Condensa 0.683 frontotemporal-dementia -
Seed match plus local RNA structure jointly determine lncRNA 0.670 molecular-neurobiology How does lncRNA-0021 achieve sequence-sp
m6A Hypermethylation of SNCA mRNA Stabilises Alpha-Synuclein 0.662 parkinson m6A RNA Modification and Alpha-Synuclein
RNA Granule Nucleation Site Modulation 0.662 neurodegeneration TDP-43 phase separation therapeutics for
Mitochondrial RNA Granule Rescue Pathway 0.656 neurodegeneration RNA binding protein dysregulation across
RNA-binding protein condensate maturation from reversible ph 0.626 neurodegeneration Causal Sequence of TDP-43 Nuclear Cleara
RNA-binding protein condensate maturation from reversible ph 0.626 neurodegeneration Biophysical Determinants Shifting FUS/TD
m6A-dependent control of alpha-synuclein transcript fate and 0.626 neurodegeneration m6A RNA Modification and Alpha-Synuclein
H7: Aberrant RNA Template Switching Converts Granules to Agg 0.625 neurodegeneration How do pathological stress granules tran
Integrated Blood Panel of sPDGFRβ, sTM, and Circulating micr 0.625 - What blood-brain barrier permeability ch
RNA-Binding Protein Sequestration and 3′UTR Dysregulation 0.625 - How does the intron-retained RNA isoform
Synaptic RNA Metabolism Dysregulation 0.620 neurodegeneration What mechanisms underlie TDP-43's contri
Trinucleotide Repeat Sequestration via CRISPR-Guided RNA Tar 0.613 neurodegeneration CRISPR-based therapeutic approaches for
Cell-state stratification is required to resolve m6A RNA Mod 0.612 neurodegeneration m6A RNA Modification and Alpha-Synuclein
Perturbation-first validation should precede therapeutic cla 0.608 neurodegeneration m6A RNA Modification and Alpha-Synuclein

Mentioning Analyses (16)

Scientific analyses that reference this entity

Biophysical Determinants Shifting FUS/TDP-43 Phase Separation to Pathological Ag

neurodegeneration | 2026-04-27 | 4 hypotheses Top: 0.680

m6A RNA Modification and Alpha-Synuclein Aggregation in Substantia Nigra

neurodegeneration | 2026-04-27 | 4 hypotheses Top: 0.662

Non-Neuronal Transcriptional Changes Preceding Tau Propagation as Early AD Bioma

neurodegeneration | 2026-04-27 | 3 hypotheses Top: 0.626

Microglial Priming as Upstream Causal Node Across AD, PD, ALS, MS: Three-Arm Cau

neurodegeneration | 2026-04-27 | 3 hypotheses Top: 0.604

How does the intron-retained RNA isoform mechanistically reduce glucocerebrosida

neurodegeneration | 2026-04-26 | 7 hypotheses Top: 0.645

Experiments (1)

Experimental studies targeting or related to this entity

ExperimentTypeDiseaseScoreFeasibilityModelStatusEst. Cost
Autophagy receptor identification for stress granule elimination exploratory neurodegenerative diseases 0.900 0.00 cultured cells under arsenite proposed N/A

Related Papers (15)

Scientific publications cited in analyses involving this entity

Title & PMIDAuthorsJournalYearCitations
Small molecule-driven NLRP3 inflammation inhibition via interplay between ubiqui [PMID:30966861] ["Han X", "Sun S", "Sun Y", "Song Q", "Z Autophagy 2020 1
Roles of NAD+ in Health and Aging. [PMID:37848251] Lautrup S, Hou Y, Fang EF, Bohr VA Cold Spring Harbor perspective 2024 0
Inhibition of autophagy in microglia and macrophages exacerbates innate immune r [PMID:36652438] Hegdekar N, Sarkar C, Bustos S, Ritzel R Autophagy 2023 0
Inflammasome assembly in neurodegenerative diseases. [PMID:37633753] Singh J, Habean ML, Panicker N Trends in neurosciences 2023 0
The different autophagy degradation pathways and neurodegeneration. [PMID:35134347] Fleming A, Bourdenx M, Fujimaki M, Karab Neuron 2022 0
NLRP3/caspase-1/GSDMD-mediated pyroptosis exerts a crucial role in astrocyte pat [PMID:34877938] Li S, Sun Y, Song M, Song Y, Fang Y, Zha JCI insight 2021 0
WDR45 contributes to neurodegeneration through regulation of ER homeostasis and [PMID:31204559] ["Wan Huida", "Wang Qi", "Chen Xiuting", Autophagy 2020 0
WDR45 contributes to neurodegeneration through regulation of ER homeostasis and [PMID:31204559] ["Wan Huida", "Wang Qi", "Chen Xiuting", Autophagy 2020 0
Mitophagy inhibits amyloid-β and tau pathology and reverses cognitive defi [PMID:30742114] Unknown Nature neuroscience 2019 0
Inflammasome inhibition prevents α-synuclein pathology and dopaminergic neurodeg [PMID:30381407] Gordon R, Albornoz EA, Christie DC, Lang Science translational medicine 2018 0
TIA1 Mutations in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Prom [PMID:28817800] ["Mackenzie Ian R", "Nicholson Alexandra Neuron 2017 0
Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem prote [PMID:23455423] Unknown Nature 2013 0
A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-lin [PMID:21944779] Unknown Neuron 2011 0
TDP-43 immunoreactivity in hippocampal sclerosis and Alzheimer's disease. [PMID:17469117] Unknown Annals of neurology 2007 0
Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic latera [PMID:17023659] Unknown Science (New York, N.Y.) 2006 0

Debates (20)

Multi-agent debates referencing this entity

Structured research brief: Stathmin-2 Splice Switching to Prevent Axonal Degener

archived · Rounds: 2 · Score: 0.73 · 2026-04-28

Is microglial priming (TREM2/CX3CR1/complement-C1q) genuinely causally upstream

closed · Rounds: 4 · Score: 0.64 · 2026-04-28

What are the biophysical determinants — RNA binding stoichiometry, post-translat

closed · Rounds: 4 · Score: 0.67 · 2026-04-28

Which non-neuronal cell types (astrocytes, oligodendrocytes, pericytes) exhibit

closed · Rounds: 4 · Score: 0.67 · 2026-04-28

How does N6-methyladenosine (m6A) RNA modification alter alpha-synuclein mRNA st

closed · Rounds: 4 · Score: 0.67 · 2026-04-28

Hypothesis debate: Stathmin-2 Splice Switching to Prevent Axonal Degeneration Ac

closed · Rounds: 4 · Score: 0.49 · 2026-04-27

How does the intron-retained RNA isoform mechanistically reduce glucocerebrosida

closed · Rounds: 4 · Score: 1.00 · 2026-04-26

Which specific factors in conditioned medium from healthy astrocytes rescue moto

closed · Rounds: 4 · Score: 0.65 · 2026-04-25

How does lncRNA-0021 achieve sequence-specific binding to mmu-miR-6361 and what

closed · Rounds: 4 · Score: 0.66 · 2026-04-25

The ASO therapeutic hypothesis assumes dilncRNAs have targetable conserved struc

closed · Rounds: 4 · Score: 0.69 · 2026-04-21

Related Research

Hypotheses and analyses mentioning RNA in their description or question text

Calcium-Dysregulated mPTP Opening as an Alternative mtDNA Release Mechanism for

Score: 0.804 · neurodegeneration · 2026-04-05

## Mechanistic Overview Calcium-Dysregulated mPTP Opening as an Alternative mtDNA Release Mechanism for AIM2 Inflammasom

Stress-granule RNA-binding protein phase transition across ALS and FTD

Score: 0.780 · multi · 2026-04-28

Shared mechanism across ALS, FTD: Low-complexity RNA-binding proteins normally form reversible stress granules, but ALS/

METTL3-Mediated m6A Modification of lncRNA-0021 Regulates miR-6361 Sequestration

Score: 0.769 · molecular-neurobiology · 2026-04-17

## **Molecular Mechanism and Rationale** The methyltransferase-like 3 (METTL3) enzyme functions as the catalytic subuni

Seed-Proximal Asymmetric Duplex Stability Confers lncRNA-0021/miR-6361 Binding S

Score: 0.733 · molecular-neurobiology · 2026-04-17

**Molecular Mechanism and Rationale** The lncRNA-0021/miR-6361 interaction represents a sophisticated regulatory mechan

m6A RNA Modification as Address Code for Granule Targeting

Score: 0.700 · neurodegeneration · 2026-04-21

**Molecular Mechanism and Rationale** The N6-methyladenosine (m6A) RNA modification system represents a sophisticated c

C9orf72 repeat RNA and dipeptide-repeat toxicity in ALS/FTD

Score: 0.700 · neurodegeneration · 2026-04-29

C9orf72 hexanucleotide repeat expansion produces repeat RNA foci and RAN-translated dipeptide-repeat proteins that disru

Axonal RNA Transport Reconstitution

Score: 0.695 · neurodegeneration · 2026-04-02

## Mechanistic Overview Axonal RNA Transport Reconstitution starts from the claim that modulating HNRNPA2B1 within the d

hnRNPA2B1-Mediated Structural Remodeling Controls lncRNA-0021 Accessibility for

Score: 0.684 · molecular-neurobiology · 2026-04-17

## **Molecular Mechanism and Rationale** The proposed therapeutic mechanism centers on the regulatory interplay between

Seed match plus local RNA structure jointly determine lncRNA-0021 binding to mmu

Score: 0.670 · molecular-neurobiology · 2026-04-25

The most likely explanation is a two-factor recognition mechanism: a canonical miRNA seed-complementary site in lncRNA-0

m6A Hypermethylation of SNCA mRNA Stabilises Alpha-Synuclein Transcript and Prom

Score: 0.662 · parkinson · 2026-04-27

N6-methyladenosine (m6A) hypermethylation of SNCA mRNA in substantia nigra dopaminergic neurons stabilises the transcrip

RNA Granule Nucleation Site Modulation

Score: 0.662 · neurodegeneration · 2026-04-02

## Mechanistic Overview RNA Granule Nucleation Site Modulation starts from the claim that modulating G3BP1 within the di

Mitochondrial RNA Granule Rescue Pathway

Score: 0.656 · neurodegeneration · 2026-04-02

## Mechanistic Overview Mitochondrial RNA Granule Rescue Pathway starts from the claim that modulating SYNCRIP within th