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Fusion Gene Summary | |
Fusion Gene ORF analysis | |
Fusion Genomic Features | |
Fusion Protein Features | |
Fusion Gene Sequence | |
Fusion Gene PPI analysis | |
Related Drugs | |
Related Diseases |
Fusion gene:EGFR-LYST (FusionGDB2 ID:25471) |
Fusion Gene Summary for EGFR-LYST |
Fusion gene summary |
Fusion gene information | Fusion gene name: EGFR-LYST | Fusion gene ID: 25471 | Hgene | Tgene | Gene symbol | EGFR | LYST | Gene ID | 1956 | 1130 |
Gene name | epidermal growth factor receptor | lysosomal trafficking regulator | |
Synonyms | ERBB|ERBB1|HER1|NISBD2|PIG61|mENA | CHS|CHS1 | |
Cytomap | 7p11.2 | 1q42.3 | |
Type of gene | protein-coding | protein-coding | |
Description | epidermal growth factor receptoravian erythroblastic leukemia viral (v-erb-b) oncogene homologcell growth inhibiting protein 40cell proliferation-inducing protein 61epidermal growth factor receptor tyrosine kinase domainerb-b2 receptor tyrosine kinas | lysosomal-trafficking regulatorChediak-Higashi syndrome 1beige homolog | |
Modification date | 20200329 | 20200313 | |
UniProtAcc | P00533 | Q99698 | |
Ensembl transtripts involved in fusion gene | ENST00000463948, ENST00000275493, ENST00000342916, ENST00000344576, ENST00000420316, ENST00000442591, ENST00000455089, ENST00000454757, | ENST00000389793, ENST00000389794, ENST00000536965, ENST00000473037, | |
Fusion gene scores | * DoF score | 41 X 25 X 14=14350 | 8 X 8 X 5=320 |
# samples | 53 | 8 | |
** MAII score | log2(53/14350*10)=-4.75891456699985 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/320*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Context | PubMed: EGFR [Title/Abstract] AND LYST [Title/Abstract] AND fusion [Title/Abstract] | ||
Most frequent breakpoint | EGFR(55087058)-LYST(235996967), # samples:3 | ||
Anticipated loss of major functional domain due to fusion event. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | EGFR | GO:0001934 | positive regulation of protein phosphorylation | 20551055 |
Hgene | EGFR | GO:0007165 | signal transduction | 10572067 |
Hgene | EGFR | GO:0007166 | cell surface receptor signaling pathway | 7736574 |
Hgene | EGFR | GO:0007173 | epidermal growth factor receptor signaling pathway | 7736574|12435727 |
Hgene | EGFR | GO:0008283 | cell proliferation | 17115032 |
Hgene | EGFR | GO:0008284 | positive regulation of cell proliferation | 7736574 |
Hgene | EGFR | GO:0010750 | positive regulation of nitric oxide mediated signal transduction | 12828935 |
Hgene | EGFR | GO:0018108 | peptidyl-tyrosine phosphorylation | 22732145 |
Hgene | EGFR | GO:0030307 | positive regulation of cell growth | 15467833 |
Hgene | EGFR | GO:0042177 | negative regulation of protein catabolic process | 17115032 |
Hgene | EGFR | GO:0042327 | positive regulation of phosphorylation | 15082764 |
Hgene | EGFR | GO:0043406 | positive regulation of MAP kinase activity | 10572067 |
Hgene | EGFR | GO:0045739 | positive regulation of DNA repair | 17115032 |
Hgene | EGFR | GO:0045740 | positive regulation of DNA replication | 17115032 |
Hgene | EGFR | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20551055 |
Hgene | EGFR | GO:0050679 | positive regulation of epithelial cell proliferation | 10572067 |
Hgene | EGFR | GO:0050999 | regulation of nitric-oxide synthase activity | 12828935 |
Hgene | EGFR | GO:0070141 | response to UV-A | 18483258 |
Hgene | EGFR | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 20551055 |
Hgene | EGFR | GO:0071392 | cellular response to estradiol stimulus | 20551055 |
Hgene | EGFR | GO:1900020 | positive regulation of protein kinase C activity | 22732145 |
Hgene | EGFR | GO:1903078 | positive regulation of protein localization to plasma membrane | 22732145 |
Fusion gene breakpoints across EGFR (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
Fusion gene breakpoints across LYST (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
ChimerDB4 | LIHC | TCGA-2Y-A9H0-01A | EGFR | chr7 | 55087058 | - | LYST | chr1 | 235996967 | - |
ChimerDB4 | LIHC | TCGA-2Y-A9H0-01A | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
ChimerDB4 | LIHC | TCGA-2Y-A9H0 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
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Fusion Gene ORF analysis for EGFR-LYST |
Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
3UTR-5UTR | ENST00000463948 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
3UTR-5UTR | ENST00000463948 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
3UTR-5UTR | ENST00000463948 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
3UTR-intron | ENST00000463948 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000275493 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000275493 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000275493 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000342916 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000342916 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000342916 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000344576 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000344576 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000344576 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000420316 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000420316 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000420316 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000442591 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000442591 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000442591 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000455089 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000455089 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-5UTR | ENST00000455089 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-intron | ENST00000275493 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-intron | ENST00000342916 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-intron | ENST00000344576 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-intron | ENST00000420316 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-intron | ENST00000442591 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
5CDS-intron | ENST00000455089 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
intron-5UTR | ENST00000454757 | ENST00000389793 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
intron-5UTR | ENST00000454757 | ENST00000389794 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
intron-5UTR | ENST00000454757 | ENST00000536965 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
intron-intron | ENST00000454757 | ENST00000473037 | EGFR | chr7 | 55087058 | + | LYST | chr1 | 235996967 | - |
ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for EGFR-LYST |
FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for EGFR-LYST |
Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:55087058/:235996967) - 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. |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
EGFR | LYST |
FUNCTION: Receptor tyrosine kinase binding ligands of the EGF family and activating several signaling cascades to convert extracellular cues into appropriate cellular responses (PubMed:2790960, PubMed:10805725, PubMed:27153536). Known ligands include EGF, TGFA/TGF-alpha, AREG, epigen/EPGN, BTC/betacellulin, epiregulin/EREG and HBEGF/heparin-binding EGF (PubMed:2790960, PubMed:7679104, PubMed:8144591, PubMed:9419975, PubMed:15611079, PubMed:12297049, PubMed:27153536, PubMed:20837704, PubMed:17909029). Ligand binding triggers receptor homo- and/or heterodimerization and autophosphorylation on key cytoplasmic residues. The phosphorylated receptor recruits adapter proteins like GRB2 which in turn activates complex downstream signaling cascades. Activates at least 4 major downstream signaling cascades including the RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC and STATs modules (PubMed:27153536). May also activate the NF-kappa-B signaling cascade (PubMed:11116146). Also directly phosphorylates other proteins like RGS16, activating its GTPase activity and probably coupling the EGF receptor signaling to the G protein-coupled receptor signaling (PubMed:11602604). Also phosphorylates MUC1 and increases its interaction with SRC and CTNNB1/beta-catenin (PubMed:11483589). Positively regulates cell migration via interaction with CCDC88A/GIV which retains EGFR at the cell membrane following ligand stimulation, promoting EGFR signaling which triggers cell migration (PubMed:20462955). Plays a role in enhancing learning and memory performance (By similarity). {ECO:0000250|UniProtKB:Q01279, ECO:0000269|PubMed:10805725, ECO:0000269|PubMed:11116146, ECO:0000269|PubMed:11483589, ECO:0000269|PubMed:11602604, ECO:0000269|PubMed:12297049, ECO:0000269|PubMed:12297050, ECO:0000269|PubMed:12620237, ECO:0000269|PubMed:12873986, ECO:0000269|PubMed:15374980, ECO:0000269|PubMed:15590694, ECO:0000269|PubMed:15611079, ECO:0000269|PubMed:17115032, ECO:0000269|PubMed:17909029, ECO:0000269|PubMed:19560417, ECO:0000269|PubMed:20462955, ECO:0000269|PubMed:20837704, ECO:0000269|PubMed:21258366, ECO:0000269|PubMed:27153536, ECO:0000269|PubMed:2790960, ECO:0000269|PubMed:7679104, ECO:0000269|PubMed:8144591, ECO:0000269|PubMed:9419975}.; FUNCTION: Isoform 2 may act as an antagonist of EGF action.; FUNCTION: (Microbial infection) Acts as a receptor for hepatitis C virus (HCV) in hepatocytes and facilitates its cell entry. Mediates HCV entry by promoting the formation of the CD81-CLDN1 receptor complexes that are essential for HCV entry and by enhancing membrane fusion of cells expressing HCV envelope glycoproteins. {ECO:0000269|PubMed:21516087}. | FUNCTION: Adapter protein that regulates and/or fission of intracellular vesicles such as lysosomes (PubMed:11984006, PubMed:25216107). Might regulate trafficking of effectors involved in exocytosis (PubMed:25425525). In cytotoxic T-cells and natural killer (NK) cells, has role in the regulation of size, number and exocytosis of lytic granules (PubMed:26478006). In macrophages and dendritic cells, regulates phagosome maturation by controlling the conversion of early phagosomal compartments into late phagosomes (By similarity). In macrophages and dendritic cells, specifically involved in TLR3- and TLR4-induced production of pro-inflammatory cytokines by regulating the endosomal TLR3- TICAM1/TRIF and TLR4- TICAM1/TRIF signaling pathways (PubMed:27881733). {ECO:0000250|UniProtKB:P97412, ECO:0000269|PubMed:11984006, ECO:0000269|PubMed:25216107, ECO:0000269|PubMed:25425525, ECO:0000269|PubMed:26478006, ECO:0000269|PubMed:27881733}. |
Retention 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 * Minus value of BPloci means that the break pointn is located before the CDS. |
- In-frame and retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
- In-frame and not-retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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Fusion Gene Sequence for EGFR-LYST |
For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for EGFR-LYST |
Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
Hgene | Hgene's interactors | Tgene | Tgene's interactors |
- Retained PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
- Lost PPIs in in-frame fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
- Retained PPIs, but lost function due to frame-shift fusion. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for EGFR-LYST |
Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for EGFR-LYST |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |