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Center for Computational Systems Medicine
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Kinase Fusion Gene Summary

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Kinase Fusion Gene Sample Information

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Kinase Fusion ORF Analysis

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Kinase Fusion Amino Acid Sequences

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Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase Fusion Protein Functional Features

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Kinase Fusion Protein Structures

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Comparison of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

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pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.

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Ramachandran Plot of Kinase Fusion Protein Structure

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Potential Active Site Information

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Virtual Screening Results

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Kinase-Substrate Information

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Related Drugs with This Kinase Fusion Protein

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Related Disease with This Kinase Fusion Protein

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Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:RPL7A_NTRK1

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: RPL7A_NTRK1
KinaseFusionDB ID: KFG5519
FusionGDB2.0 ID: KFG5519
HgeneTgene
Gene symbol

RPL7A

NTRK1

Gene ID

6130

4914

Gene nameribosomal protein L7aneurotrophic receptor tyrosine kinase 1
SynonymsL7A|SURF3|TRUP|eL8MTC|TRK|TRK1|TRKA|Trk-A|p140-TrkA
Cytomap

9q34.2

1q23.1

Type of geneprotein-codingprotein-coding
Descriptionlarge ribosomal subunit protein eL860S ribosomal protein L7aPLA-X polypeptidesurfeit 3surfeit locus protein 3thyroid hormone receptor uncoupling proteinhigh affinity nerve growth factor receptorOncogene TRKTRK1-transforming tyrosine kinase proteingp140trkneurotrophic tyrosine kinase, receptor, type 1tropomyosin receptor kinase Atropomyosin-related kinase Atyrosine kinase receptor A
Modification date2024040720240411
UniProtAcc

P62424

P04629

Ensembl transtripts involved in fusion geneENST idsENST00000463740, ENST00000323345, 
ENST00000315731, 
ENST00000358660, 
ENST00000368196, ENST00000392302, 
ENST00000524377, ENST00000531606, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: RPL7A [Title/Abstract] AND NTRK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RPL7A(136215897)-NTRK1(156844362), # samples:1
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneNTRK1

GO:0006468

protein phosphorylation

15488758

TgeneNTRK1

GO:0008285

negative regulation of cell population proliferation

15488758

TgeneNTRK1

GO:0010976

positive regulation of neuron projection development

15488758

TgeneNTRK1

GO:0018108

peptidyl-tyrosine phosphorylation

2927393

TgeneNTRK1

GO:0043547

positive regulation of GTPase activity

15488758

TgeneNTRK1

GO:0046579

positive regulation of Ras protein signal transduction

15488758

TgeneNTRK1

GO:0046777

protein autophosphorylation

15488758

TgeneNTRK1

GO:0048011

neurotrophin TRK receptor signaling pathway

15488758

TgeneNTRK1

GO:0051092

positive regulation of NF-kappaB transcription factor activity

15488758

TgeneNTRK1

GO:0070374

positive regulation of ERK1 and ERK2 cascade

15488758

TgeneNTRK1

GO:1904646

cellular response to amyloid-beta

11927634


check buttonKinase Fusion gene breakpoints across RPL7A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonKinase Fusion gene breakpoints across NTRK1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Kinase Fusion Gene Sample Information

check buttonKinase Fusion gene information.
check button Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceSampleHgeneHchrHbpTgeneTchrTbp
ChiTaRS5.0X06704RPL7Achr9

136215897

NTRK1chr1

156844362



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Kinase Fusion ORF Analysis


check buttonKinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(amino acids)
ENST00000323345ENST00000392302RPL7Achr9136215897NTRK1chr11568443621502439

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Kinase Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

>ENST00000323345_ENST00000392302_RPL7A_chr9_136215897_NTRK1_chr1_156844362_length(amino acids)=439
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIDTNSTSGDPVEKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKCGRRNK
FGINRPAVLAPEDGLAMSLHFMTLGGSSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQD
KMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQL
LAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVL

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Multiple Sequence Alignment of All Fusion Protein Isoforms



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Kinase Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:136215897/chr1:156844362)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RPL7A

P62424

NTRK1

P04629

FUNCTION: Component of the large ribosomal subunit (PubMed:23636399, PubMed:32669547). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23636399, PubMed:32669547). {ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:32669547}.FUNCTION: Receptor tyrosine kinase involved in the development and the maturation of the central and peripheral nervous systems through regulation of proliferation, differentiation and survival of sympathetic and nervous neurons. High affinity receptor for NGF which is its primary ligand (PubMed:1850821, PubMed:1849459, PubMed:1281417, PubMed:8325889, PubMed:15488758, PubMed:22649032, PubMed:17196528, PubMed:27445338). Can also bind and be activated by NTF3/neurotrophin-3. However, NTF3 only supports axonal extension through NTRK1 but has no effect on neuron survival (By similarity). Upon dimeric NGF ligand-binding, undergoes homodimerization, autophosphorylation and activation (PubMed:1281417). Recruits, phosphorylates and/or activates several downstream effectors including SHC1, FRS2, SH2B1, SH2B2 and PLCG1 that regulate distinct overlapping signaling cascades driving cell survival and differentiation. Through SHC1 and FRS2 activates a GRB2-Ras-MAPK cascade that regulates cell differentiation and survival. Through PLCG1 controls NF-Kappa-B activation and the transcription of genes involved in cell survival. Through SHC1 and SH2B1 controls a Ras-PI3 kinase-AKT1 signaling cascade that is also regulating survival. In absence of ligand and activation, may promote cell death, making the survival of neurons dependent on trophic factors. {ECO:0000250|UniProtKB:P35739, ECO:0000250|UniProtKB:Q3UFB7, ECO:0000269|PubMed:11244088, ECO:0000269|PubMed:1281417, ECO:0000269|PubMed:15488758, ECO:0000269|PubMed:17196528, ECO:0000269|PubMed:1849459, ECO:0000269|PubMed:1850821, ECO:0000269|PubMed:22649032, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:27676246, ECO:0000269|PubMed:8155326, ECO:0000269|PubMed:8325889}.; FUNCTION: [Isoform TrkA-III]: Resistant to NGF, it constitutively activates AKT1 and NF-kappa-B and is unable to activate the Ras-MAPK signaling cascade. Antagonizes the anti-proliferative NGF-NTRK1 signaling that promotes neuronal precursors differentiation. Isoform TrkA-III promotes angiogenesis and has oncogenic activity when overexpressed. {ECO:0000269|PubMed:15488758}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.

check button - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


check button - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote
TgeneRPL7A136215897NTRK1156844362ENST00000323345716510_781392791DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
TgeneRPL7A136215897NTRK1156844362ENST00000323345817510_781362761DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
TgeneRPL7A136215897NTRK1156844362ENST00000323345817510_781398797DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159


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Kinase Fusion Protein Structures

check button CIF files of the predicted kinase fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Kinase Fusion protein CIF link (fusion AA seq ID in KinaseFusionDB)HenstTenstHgeneHchrHbpTgeneTchrTbpAA seqLen(AA seq)
PDB file >>>427_RPL7A_NTRK1ENST00000323345ENST00000392302RPL7Achr9136215897NTRK1chr1156844362
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIDTNSTSGDPVEKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKCGRRNK
FGINRPAVLAPEDGLAMSLHFMTLGGSSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQD
KMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQL
LAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVL
439
3D view using mol* of 427_RPL7A_NTRK1
PDB file >>>TKFP_713_RPL7A_NTRK1ENST00000323345ENST00000392302RPL7Achr9136215897NTRK1chr1156844362
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIDTNSTSGDPVEKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKCGRRNK
FGINRPAVLAPEDGLAMSLHFMTLGGSSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQD
KMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQL
LAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVL
439_RPL7A_NTRK1


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Comparison of Fusion Protein Isoforms

check button Superimpose the 3D Structures Among All Fusion Protein Isoforms
* Download the pdb file and open it from the molstar online viewer.

check button Comparison of the Secondary Structures of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

RPL7A_NTRK1 does not have any known PDB structures.

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pLDDT score distribution

all_data/KinaseFusionDB_T_Results/KinaseFusionDB_T_ViolinPlots/427_RPL7A_NTRK1.png
check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
* The blue color at the bottom marks the best active site residues.
427_RPL7A_NTRK1.png
all structure sitemap plddt3 427_RPL7A_NTRK1.png
427_RPL7A_NTRK1.png
all structure sitemap plddt4 427_RPL7A_NTRK1.png


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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Kinase Fusion AA seq ID in KinaseFusionDBSite scoreSizeDscoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues

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Ramachandran Plot of Kinase Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

427_RPL7A_NTRK1_ramachandran.png
all structure RPL7A-NTRK1

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Virtual Screening Results


check button Distribution of the average docking score across all approved kinase inhibitors.
Distribution of the number of occurrence across all approved kinase inhibitors.
5'-kinase fusion protein case
3'-kinase fusion protein case

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check button Drug information from DrugBank of the top 20 interacting small molecules.
* The detailed information of individual kinase inhibitors are available in the download page.
Fusion gene name infoDrugDocking scoreGlide g scoreGlide energy

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Kinase-Substrate Information of RPL7A_NTRK1


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
NTRK1P04629humanSH2B1Q9NRF2Y753PRAINNQySFV____
NTRK1P04629humanCTNNB1P35222Y142AVVNLINyQDDAELA
NTRK1P04629humanNTRK1P04629-2Y490HIIENPQyFSDACVH
NTRK1P04629humanNTRK1P04629-2Y674RDIySTDyyRVGGRTPK_Tyr_Ser-Thr
NTRK1P04629humanNTRK1P04629Y680RDIySTDyyRVGGRTPK_Tyr_Ser-Thr
NTRK1P04629humanSHC3Q92529-2Y218GDGSDHPyyNSIPSK
NTRK1P04629humanSHC3Q92529-2Y256FAGKEQTyyQGRHLG
NTRK1P04629humanNTRK1P04629-2Y670FGMSRDIySTDyyRVPK_Tyr_Ser-Thr
NTRK1P04629humanNTRK1P04629Y496HIIENPQyFSDACVH
NTRK1P04629humanSTAT3P40763Y705DPGsAAPyLktKFIC
NTRK1P04629humanSHC1P29353-2Y317ELFDDPSyVNVQNLD
NTRK1P04629humanPLCG1P19174Y771IGtAEPdyGALyEGR
NTRK1P04629humanPLCG1P19174Y783EGRNPGFyVEANPMP
NTRK1P04629humanNTRK1P04629-2Y675DIySTDyyRVGGRTMPK_Tyr_Ser-Thr
NTRK1P04629humanNTRK1P04629-2Y751RACPPEVyAIMRGCWPK_Tyr_Ser-Thr
NTRK1P04629humanNTRK1P04629Y681DIySTDyyRVGGRTMPK_Tyr_Ser-Thr
NTRK1P04629humanNTRK1P04629-2Y785LAQAPPVyLDVLG__
NTRK1P04629humanSHC3Q92529-2Y301PTGEAPTyVNTQQIP
NTRK1P04629humanSHC3Q92529-2Y257AGKEQTyyQGRHLGD
NTRK1P04629humanSHC3Q92529-2Y283RQGSSDIySTPEGKL
NTRK1P04629humanSHC3Q92529-2Y219DGSDHPyyNSIPSKM


check button Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

check button Enriched GO biological processes of the phosphorylation target genes of the kinase
KinaseGOIDGO termP.adjust
NTRK1IDDescription0.00e+00
NTRK1GO:0007173epidermal growth factor receptor signaling pathway3.89e-03
NTRK1GO:0038127ERBB signaling pathway3.89e-03
NTRK1GO:0048485sympathetic nervous system development7.40e-03
NTRK1GO:1905564positive regulation of vascular endothelial cell proliferation8.42e-03
NTRK1GO:0050679positive regulation of epithelial cell proliferation8.42e-03
NTRK1GO:0051091positive regulation of DNA-binding transcription factor activity9.81e-03
NTRK1GO:0048483autonomic nervous system development1.32e-02
NTRK1GO:0101023vascular endothelial cell proliferation1.32e-02
NTRK1GO:1905562regulation of vascular endothelial cell proliferation1.32e-02
NTRK1GO:0050982detection of mechanical stimulus1.32e-02
NTRK1GO:0045765regulation of angiogenesis1.43e-02
NTRK1GO:1901342regulation of vasculature development1.43e-02
NTRK1GO:0021545cranial nerve development1.43e-02
NTRK1GO:0051090regulation of DNA-binding transcription factor activity1.78e-02
NTRK1GO:0050678regulation of epithelial cell proliferation1.78e-02
NTRK1GO:0030098lymphocyte differentiation1.95e-02
NTRK1GO:0043410positive regulation of MAPK cascade2.21e-02
NTRK1GO:0050673epithelial cell proliferation2.21e-02
NTRK1GO:1903131mononuclear cell differentiation2.21e-02
NTRK1GO:0021675nerve development2.21e-02
NTRK1GO:0001938positive regulation of endothelial cell proliferation2.65e-02
NTRK1GO:0032355response to estradiol2.65e-02
NTRK1GO:0051963regulation of synapse assembly2.65e-02
NTRK1GO:2000278regulation of DNA biosynthetic process2.67e-02
NTRK1GO:0048593camera-type eye morphogenesis3.31e-02
NTRK1GO:0009581detection of external stimulus3.42e-02
NTRK1GO:0009582detection of abiotic stimulus3.44e-02
NTRK1GO:0051092positive regulation of NF-kappaB transcription factor activity3.62e-02
NTRK1GO:0048592eye morphogenesis3.62e-02
NTRK1GO:0043524negative regulation of neuron apoptotic process3.62e-02
NTRK1GO:0046661male sex differentiation3.62e-02
NTRK1GO:0001764neuron migration3.62e-02
NTRK1GO:0001936regulation of endothelial cell proliferation3.62e-02
NTRK1GO:0019827stem cell population maintenance3.62e-02
NTRK1GO:0045766positive regulation of angiogenesis3.62e-02
NTRK1GO:1904018positive regulation of vasculature development3.62e-02
NTRK1GO:0098727maintenance of cell number3.62e-02
NTRK1GO:0071897DNA biosynthetic process3.62e-02
NTRK1GO:0007416synapse assembly3.62e-02
NTRK1GO:0001935endothelial cell proliferation3.62e-02
NTRK1GO:0050728negative regulation of inflammatory response3.62e-02
NTRK1GO:0009612response to mechanical stimulus3.62e-02
NTRK1GO:0045637regulation of myeloid cell differentiation3.62e-02
NTRK1GO:1901888regulation of cell junction assembly3.62e-02
NTRK1GO:0070374positive regulation of ERK1 and ERK2 cascade3.62e-02
NTRK1GO:0043523regulation of neuron apoptotic process3.62e-02
NTRK1GO:0050807regulation of synapse organization3.62e-02
NTRK1GO:0048863stem cell differentiation3.62e-02
NTRK1GO:0050803regulation of synapse structure or activity3.62e-02

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Related Drugs to RPL7A_NTRK1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

check button Distribution of the number of studies mentioning RPL7A-NTRK1 and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1Fusion gene - drug pair 2PMIDPublication dateDOIStudy title

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Related Diseases to RPL7A_NTRK1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)
MeSH IDMeSH term

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneNTRK1C0020074HSAN Type IV17CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNTRK1C0238463Papillary thyroid carcinoma3ORPHANET


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Clinical Trials of the Found Drugs/Small Molecules


check button Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

check button Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion GeneKinase InhibitorNCT IDStudy StatusPhasesDisease# EnrolmentDate