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Fusion gene ID: 4364 |
FusionGeneSummary for BRAF_MED4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: BRAF_MED4 | Fusion gene ID: 4364 | Hgene | Tgene | Gene symbol | BRAF | MED4 | Gene ID | 673 | 29079 |
| Gene name | B-Raf proto-oncogene, serine/threonine kinase | mediator complex subunit 4 | |
| Synonyms | B-RAF1|B-raf|BRAF1|NS7|RAFB1 | ARC36|DRIP36|HSPC126|TRAP36|VDRIP | |
| Cytomap | 7q34 | 13q14.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | serine/threonine-protein kinase B-raf94 kDa B-raf proteinB-Raf proto-oncogene serine/threonine-protein kinase (p94)B-Raf serine/threonine-proteinmurine sarcoma viral (v-raf) oncogene homolog B1proto-oncogene B-Rafv-raf murine sarcoma viral oncogene | mediator of RNA polymerase II transcription subunit 4TRAP/SMCC/PC2 subunit p36activator-recruited cofactor 36 kDa componentmediator, 34-kD subunit, homologvitamin D receptor-interacting protein, 36-kDvitamin D3 receptor-interacting protein complex 36 | |
| Modification date | 20180527 | 20180523 | |
| UniProtAcc | P15056 | Q9NPJ6 | |
| Ensembl transtripts involved in fusion gene | ENST00000288602, | ENST00000495013, ENST00000258648, ENST00000378586, | |
| Fusion gene scores | * DoF score | 18 X 12 X 10=2160 | 6 X 2 X 5=60 |
| # samples | 22 | 7 | |
| ** MAII score | log2(22/2160*10)=-3.29545588352617 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/60*10)=0.222392421336448 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: BRAF [Title/Abstract] AND MED4 [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 | BRAF | GO:0006468 | protein phosphorylation | 17563371 |
| Hgene | BRAF | GO:0010828 | positive regulation of glucose transmembrane transport | 23010278 |
| Hgene | BRAF | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 19667065 |
| Hgene | BRAF | GO:0043066 | negative regulation of apoptotic process | 19667065 |
| Hgene | BRAF | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 22065586 |
| Hgene | BRAF | GO:0071277 | cellular response to calcium ion | 18567582 |
| Hgene | BRAF | GO:0090150 | establishment of protein localization to membrane | 23010278 |
| Tgene | MED4 | GO:0006366 | transcription by RNA polymerase II | 10882111 |
| Tgene | MED4 | GO:0006367 | transcription initiation from RNA polymerase II promoter | 12218053 |
| Tgene | MED4 | GO:0030518 | intracellular steroid hormone receptor signaling pathway | 11867769 |
| Tgene | MED4 | GO:0030521 | androgen receptor signaling pathway | 12218053 |
| Tgene | MED4 | GO:0045893 | positive regulation of transcription, DNA-templated | 10198638 |
| 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 | SARC | TCGA-DX-A8BM-01A | BRAF | chr7 | 140501212 | - | MED4 | chr13 | 48664554 | - |
| * 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 | ENST00000288602 | ENST00000495013 | BRAF | chr7 | 140501212 | - | MED4 | chr13 | 48664554 | - |
| 5CDS-intron | ENST00000288602 | ENST00000258648 | BRAF | chr7 | 140501212 | - | MED4 | chr13 | 48664554 | - |
| 5CDS-5UTR | ENST00000288602 | ENST00000378586 | BRAF | chr7 | 140501212 | - | MED4 | chr13 | 48664554 | - |
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FusionProtFeatures for BRAF_MED4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| BRAF | MED4 |
| 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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FusionGeneSequence for BRAF_MED4 |
| 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). |
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FusionGenePPI for BRAF_MED4 |
| 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 |
| BRAF | YWHAB, YWHAG, YWHAQ, YWHAZ, SFN, HRAS, AKT1, MAPK3, RAP1GAP, RAF1, MRAS, RAP1A, PAK2, TERF1, CCDC88A, NEDD4L, MAP2K1, RNF149, KSR1, BRAP, PRKCE, RPS6KB2, HSP90AA1, BRAF, YWHAE, HSPA5, MAP2K2, HSPA1A, HSPA8, YWHAH, HSPA9, ARAF, CDC37, HSP90AB1, PHKB, LIMK1, IQGAP1, MAPK1, BAD, LIPF, MUS81, FBXW7, FGFR2, BRCA2, VHL, FNTA, HDAC2, PIK3CA, EGFR, PTEN, FNIP1, FNIP2, RAB3GAP1, KRAS, KIAA0141, FKBPL, ARMCX3, KCNC4, RPTOR, CYLD, NRAS | MED4 | TNFAIP8, AP2M1, MCRS1, MED10, MED9, MED29, MED19, MED28, MED26, MED30, MED1, RPAP2, PCBD2, MED18, EMD, MED12, ZC3H13, TRIP4, OBFC1, QKI, TADA2A, VDR, CTDP1, PUM2, MED13, WDTC1, FOXJ3, ELAVL1, COPS2, MED6, MED8, MED14, MED16, MED24, MED11, MED27, MED21, MED22, NIFK, FBXW7, EPAS1, ESR2, CDK8, CDK19, RPA3, RPA2, RPA1, NDE1, AES, KIFC3, SDCBP, SMARCD1, SMARCE1, LRRFIP1, SSX3, NDC80, FTCD, CCHCR1, CTNNBL1, CCDC146, USHBP1, IFT20, CCDC101, HAUS1, FRMD6, MAB21L3, C1orf216, AMOT, TXLNA, FAM13C, NXF1, MED7, CCNC, SEC13, NR1I3, TCL1B, MED17, HUWE1, MED15, MED20, PPM1G, PCM1, CEP131, OFD1, CCDC138, HAUS6, PCNT, AHNAK, PIBF1, CCDC14, KIAA0753, HAUS5, HAUS3, CD2AP, CEP170, MIB1, GIT1, CCDC18, KIF7, HAUS4, CEP350, NBN, FLNB, CEP290, KIF3A, MED13L, SQSTM1, KIF5B, CKAP5, TBC1D31, CEP72, DVL2, SSX2IP, HAUS8, MYCBP2, CEP55, POLR2A, XRN1, ERC1, EXOC4, LUZP1, ARHGEF7, ANKRD26, DCTN2, KIF11, CSPP1, GIT2, ACTR1A, EPB41L3, SRP68, CCDC61, CEP162, NSFL1C, ADSL, TLN1, EDRF1, SLK, SPAG5, MAP1B, HAUS2, MPHOSPH9, CCDC77, NIN, CEP152, DBT, DLG5, RAI14, KIF5A, TBK1, PSMD7, ODF2, PAICS, IFT74, TP53BP2, ECD, HAUS7, TXLNG, MAP7D3, CCP110, MED31, SPICE1, TTLL5, IFIT5, ATG2B, EPS15L1, SPAG9, CCDC66, CLINT1, KEAP1, MICAL3, ODF2L, UBE2O, CAMSAP1, EDC4, IFT81, SDCCAG3, PSMA2, TRIM25, ALMS1, SKA3, CCDC22, WRAP73, SPC24, BUB1B, CNOT10, LRBA, PDLIM5, UTRN, WDR90, CNOT1, CNTROB, KIAA1598, CNOT11, EIF3M, EPB41, WNK1, TTC28, C2CD3, CYLD, DCTN3, DPYSL3, ERBB2IP, FAM101B, KANK2, KIAA1524, LSM12, PSMB1, RBM11, SH3GLB2, SNX1, USP15, ZFYVE16, ZYX, PDIA6, CEP135, CPSF3, FAM111B, FAM91A1, KIF14, SCRIB, SNAP29, DENND4C, DST, FGFR1OP, NAV1, NEK9, TCHP, MED23, ATP5F1, PDCD6, AMD1, DHX40, LARP7, MOGS, NUFIP2, SCO1, ZC3H15, DNAJB1, RRP1, SRSF5, TNRC6B, ATP5H, SDE2, EEF1E1, FIP1L1, GLYR1, GNAO1, HBB, MESDC2, MRPS17, NOP2, PIP4K2A, RAB5A, RANBP9, SEC61A1, TAX1BP1, TXNDC9, WDR33, BAG6, CSNK2A2, ATPIF1, LRRC47, CRIPT, AP2A1, ATP6V1B2, HBA2, MRRF, ZMAT2, MED25, NCAPG, GTF2F1, FAM50A, CAP2, SRRM1, ARRB2, BRIX1, EXOC1, NOP56, PMAIP1, CYCS, MANF, EXOSC8, SPTAN1, CDK11A, F5, RBM27, SUPT16H, XRCC4, CP, HADHB, A2M, SERF1A, ZNF638, CORO1C, THOC2, GLUD2, RSL1D1, SSNA1, KARS, ARHGEF6, MOB2, PIP5K1A, FLII, SKA1, TCEA1, SNRPG, ALB, HPX, DZIP3, ERCC3, RBM14, HOMER1, RNPS1, RSRC2, ATP5C1, CPSF7, HSPBP1, PIP4K2B, POLR2B, PI4KA, C3, PIP4K2C, QPCT, MRFAP1, MAP3K7, GTF2B, HADHA, PSME3, PDAP1, UBAP2L, THRAP3, BCLAF1, ACAP2, RAE1, RIOK1, CCAR1, EWSR1, AHI1, CEP120, CEP128, CEP63, CEP89, CNTRL, POC5, LCA5, SASS6, KRAS, MYH11, POLR2G, KIF21B, PTPN22, TPTE2, TXLNB, PSMC5, BIRC5, LRRCC1, TRIP11, CHPF |
| - 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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RelatedDrugs for BRAF_MED4 |
| 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 |
| Hgene | BRAF | P15056 | DB08881 | Vemurafenib | Serine/threonine-protein kinase B-raf | small molecule | approved |
| Hgene | BRAF | P15056 | DB08896 | Regorafenib | Serine/threonine-protein kinase B-raf | small molecule | approved |
| Hgene | BRAF | P15056 | DB00398 | Sorafenib | Serine/threonine-protein kinase B-raf | small molecule | approved|investigational |
| Hgene | BRAF | P15056 | DB08912 | Dabrafenib | Serine/threonine-protein kinase B-raf | small molecule | approved|investigational |
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RelatedDiseases for BRAF_MED4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | BRAF | C0025202 | melanoma | 21 | CTD_human |
| Hgene | BRAF | C1527249 | Colorectal Cancer | 8 | UNIPROT |
| Hgene | BRAF | C1275081 | Cardio-facio-cutaneous syndrome | 6 | CTD_human;ORPHANET;UNIPROT |
| Hgene | BRAF | C0009404 | Colorectal Neoplasms | 4 | CTD_human |
| Hgene | BRAF | C0040136 | Thyroid Neoplasm | 4 | CTD_human |
| Hgene | BRAF | C0024305 | Lymphoma, Non-Hodgkin | 3 | UNIPROT |
| Hgene | BRAF | C0684249 | Carcinoma of lung | 3 | UNIPROT |
| Hgene | BRAF | C3150970 | NOONAN SYNDROME 7 | 3 | CTD_human;UNIPROT |
| Hgene | BRAF | C0152013 | Adenocarcinoma of lung (disorder) | 2 | CTD_human |
| Hgene | BRAF | C0002448 | Ameloblastoma | 1 | CTD_human |
| Hgene | BRAF | C0004114 | Astrocytoma | 1 | CTD_human |
| Hgene | BRAF | C0010276 | Craniopharyngioma | 1 | CTD_human;ORPHANET |
| Hgene | BRAF | C0017638 | Glioma | 1 | CTD_human |
| Hgene | BRAF | C0022665 | Kidney Neoplasm | 1 | CTD_human |
| Hgene | BRAF | C0023903 | Liver neoplasms | 1 | CTD_human |
| Hgene | BRAF | C0024694 | Mandibular Neoplasms | 1 | CTD_human |
| Hgene | BRAF | C0028326 | Noonan Syndrome | 1 | CTD_human;ORPHANET |
| Hgene | BRAF | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Hgene | BRAF | C0036920 | Sezary Syndrome | 1 | CTD_human |
| Hgene | BRAF | C0079773 | Lymphoma, T-Cell, Cutaneous | 1 | CTD_human |
| Hgene | BRAF | C0206686 | Adrenocortical carcinoma | 1 | CTD_human |
| Hgene | BRAF | C0206754 | Neuroendocrine Tumors | 1 | CTD_human |
| Hgene | BRAF | C0238463 | Papillary thyroid carcinoma | 1 | CTD_human;ORPHANET |
| Hgene | BRAF | C0587248 | Costello syndrome (disorder) | 1 | CTD_human |
| Hgene | BRAF | C0596263 | Carcinogenesis | 1 | CTD_human |
| Hgene | BRAF | C0920269 | Microsatellite Instability | 1 | CTD_human |
| Hgene | BRAF | C2239176 | Liver carcinoma | 1 | CTD_human |
| Tgene | MED4 | C0014175 | Endometriosis | 1 | CTD_human |
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