|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 19744 |
FusionGeneSummary for LIMS1_PTP4A2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LIMS1_PTP4A2 | Fusion gene ID: 19744 | Hgene | Tgene | Gene symbol | LIMS1 | PTP4A2 | Gene ID | 3987 | 8073 |
| Gene name | LIM zinc finger domain containing 1 | protein tyrosine phosphatase type IVA, member 2 | |
| Synonyms | PINCH|PINCH-1|PINCH1 | HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b | |
| Cytomap | 2q12.3 | 1p35.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | LIM and senescent cell antigen-like-containing domain protein 1LIM and senescent cell antigen-like domains 1LIM-type zinc finger domains 1particularly interesting new Cys-His protein 1renal carcinoma antigen NY-REN-48senescent cell antigen | protein tyrosine phosphatase type IVA 2PTP(CAAXII)phosphatase of regenerating liver 2protein tyrosine phosphatase IVAprotein tyrosine phosphatase IVA2protein-tyrosine phosphatase 4a2protein-tyrosine phosphatase of regenerating liver 2 | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | P48059 | Q12974 | |
| Ensembl transtripts involved in fusion gene | ENST00000544547, ENST00000332345, ENST00000393310, ENST00000410093, ENST00000409441, ENST00000338045, ENST00000462817, ENST00000542845, ENST00000393314, | ENST00000602725, ENST00000344035, ENST00000356536, ENST00000457805, ENST00000470404, ENST00000526960, | |
| Fusion gene scores | * DoF score | 4 X 2 X 3=24 | 3 X 2 X 3=18 |
| # samples | 4 | 3 | |
| ** MAII score | log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: LIMS1 [Title/Abstract] AND PTP4A2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 | LIMS1 | GO:0045892 | negative regulation of transcription, DNA-templated | 21390327 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | LD | LUAD | TCGA-55-7995-01A | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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 |
| 5CDS-intron | ENST00000544547 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| 5CDS-5UTR | ENST00000544547 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| 5CDS-5UTR | ENST00000544547 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| 5CDS-intron | ENST00000544547 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| 5CDS-intron | ENST00000544547 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| 5CDS-5UTR | ENST00000544547 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000332345 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000332345 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000332345 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000332345 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000332345 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000332345 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000393310 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000393310 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000393310 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000393310 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000393310 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000393310 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000410093 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000410093 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000410093 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000410093 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000410093 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000410093 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000409441 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000409441 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000409441 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000409441 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000409441 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000409441 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000338045 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000338045 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000338045 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000338045 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000338045 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000338045 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000462817 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000462817 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000462817 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000462817 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000462817 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000462817 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000542845 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000542845 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000542845 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000542845 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000542845 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000542845 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000393314 | ENST00000602725 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000393314 | ENST00000344035 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000393314 | ENST00000356536 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000393314 | ENST00000457805 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-intron | ENST00000393314 | ENST00000470404 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
| intron-5UTR | ENST00000393314 | ENST00000526960 | LIMS1 | chr2 | 109151050 | + | PTP4A2 | chr1 | 32385259 | - |
Top |
FusionProtFeatures for LIMS1_PTP4A2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LIMS1 | PTP4A2 |
| Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cellsurface receptor tyrosine kinases and growth factor receptors.Involved in the regulation of cell survival, cell proliferationand cell differentiation. |
| 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 |
Top |
FusionGeneSequence for LIMS1_PTP4A2 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
Top |
FusionGenePPI for LIMS1_PTP4A2 |
| 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 |
| LIMS1 | ILK, RBBP8, LPXN, EHMT2, ACP6, NCK2, STK11, HNRNPU, MBIP, MAPT, STUB1, RSU1, TYMS, MYO18A, PARVA, PARVB, CMAS, SRRT, RABGAP1, REPS1, MYH7, PXN, TRIP6, BMP2K, PARVG, KIF22, XRCC5, TMEM132A, SGOL1, ASPM, SNW1, CDC5L, MYH4 | PTP4A2 | CNNM3, TNFAIP8, CNNM4, FNTA, FNTB, PTP4A1, USF2, RABGGTB, MYC, PON2, UNK, GNB4, SPTAN1, SPTBN1, CNNM1, EFTUD1, CNNM2, PCDHB5, FMN2, GPAA1, CYP8B1, PTP4A3, PTP4A2, FHL3, ATXN7L3B, TARBP2, PRDX4, GADD45GIP1, PRDX3, RPS19BP1, RPL22L1, RPL18A, TRIM25 |
| - 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 |
Top |
RelatedDrugs for LIMS1_PTP4A2 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for LIMS1_PTP4A2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|