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Supplementary Table 1 Supplementary Table 1: gene-fusion Category Chromosome type of fusion annotation of left partner annotations of right Fusion transcripts containing location of the partner one/both identified fusion partners § original genes other cancers HNSCC METTL13/DNM3 mRNA- 1q24.3/1q24.3 intra- METTL13 encodes for DNM3 encodes for METTL13/EIF4G3 no mRNA chromosomal methyltransferase like 13 dynamin, a member of a C1orf-9/DNM3 implicated in mRNA family of guanosine biogenesis, decay, and triphosphate (GTP)- translation control. binding proteins that associate with microtubules and are involved in vesicular transport. RCSD1/MPZL1 mRNA- 1q24.2/1q24.2 intra- RCSD1 encodes for RCSD MPZL1, also known as ATP1B1/RCSD1; no mRNA chromosomal domain containing 1 PZL, encodes for myelin MPZL1/PDE4DIP; protein. protein zero like 1, an DCAF6/MPZL1 immunoglobulin superfamily protein that specifically binds tyrosine phosphatase SHP-2 through its intracellular immunoreceptor tyrosine- based inhibitory motifs. CTNNA2/HES1 mRNA- 2p12-3/3q29 inter- CTNNA2 encodes for HES1 encodes for hes HIBCH/CTNNA2 GLIS3/CTNNA2 mRNA chromosomal catenin alfa cell-cell family bHLH PIGN/CTNNA2; translocation adhesion molecule that transcription factor 1. The MRLP35/CTNNA2 may function as a linker protein is a transcriptional POLR1A/CTNNA2 between cadherin adhesion repressor of genes that receptors and the require a bHLH protein cytoskeleton to regulate for their transcription. cell-cell adhesion and differentiation in the nervous system. ZC3H15/ITGAV mRNA- 2q32.1/2q32.1 intra- ZC3H15 encodes a ITGAV encodes the ZC3H15/SERINC1 no mRNA chromosomal potassium-dependent integrin subunit alfa V. ZC3H15/CPS1; GTPase The heterodimer ZC3H15/GULP1; consisting of alpha V and ITGAV/PDE11A; beta 3 subunits is also ITGAV/FARP2 known as the vitronectin receptor. This integrin may regulate angiogenesis and cancer progression 24 FGF12/MB21D2 mRNA- 3q28-q29/3q29 intra- FGF12 encodes fibroblast MB21D2 encodes for FGF12/SYN3; no mRNA chromosomal growth factor 12. FGF Mab-21 domain TSC22D2/FGF12; family members possess containing 2 C1orf196/FGF12 broad mitogenic and cell survival activities. This growth factor lacks the N- terminal signal sequence present in most of the FGF family members, but it contains clusters of basic residues that have been demonstrated to act as a nuclear localization signal. FLNB/ENSG0000 mRNA- 3p14.3/4 inter- FLNB encodes a member antisense lnc-TET2-4 FLNB/SLMAP; no 0245384 lncRNA chromosomal of the filamin family, CCDC66/FLNB; translocation filamin b that interacts ABHD6/FLNB with glycoprotein Ib alpha as part of the process to repair vascular injuries. C9/RCOR1 mRNA- 5p13.1/14q32.31- inter- C9 encodes for the final RCOR1 encodes a protein RICTOR/C9; no mRNA q32.32 chromosomal component of the that is well-conserved, LIFR/C9; translocation complement system downregulated at birth, FAM157A/C9 and with a specific role in determining neural cell differentiation. The encoded protein binds to the C-terminal domain of REST (repressor element- 1 silencing transcription factor). RPS6KA2/RNAS mRNA- 6q27/6q27 intra- RPS6KA2 encodes a RNASET2 encodes a RPS6KA2/PSMG4 no ET2 mRNA chromosomal member of the RSK novel member of the (ribosomal S6 kinase) Rh/T2/S-glycoprotein family of serine/threonine class of extracellular kinases. This kinase ribonucleases. contains two non-identical kinase catalytic domains and phosphorylates various substrates, including members of the mitogen- activated kinase (MAPK) signalling pathway. 25 ANK1/KAT6A mRNA- 8p11.21/8p11.21 intra- ANK1 encodes for ankirin KAT6A encodes for ANK1/FUT10; no mRNA chromosomal 1, prototype of a family of lysine acetyltransferase ANK1/ADAM7; proteins that link the 6A, a member of the NECAP1/ANK1; integral membrane proteins MOZ, YBFR2, SAS2, TMEM188/ANK1; to the underlying spectrin- TIP60 family of histone WHSC1L1/ANK1; actin cytoskeleton and play acetyltransferases that IKBKB/ANK1; key roles in activities such acts as a co-activator for KIAA0146/ANK1; as cell motility, activation, several transcription PPFIA3/ANK1; proliferation, contact and factors KAT6A/IKBKB; the maintenance of KAT6A/KLK4; specialized membrane KAT6A/MSR1; domains. KAT6A/ADAM2; KAT6A/GOT1L1; KAT6A/RAB11F1P1 FAM49B/KAT6A; CHD7/KAT6A; CREBBP/KAT6A PVT1/ENSG0000 lncRNA- 8q24.21/8 intra- This gene represents a long intergenic LNC- no no 0253288 lncRNA chromosomal non-coding RNA locus that FAM135B-1:1 has been identified as a candidate oncogene. CD274/PDCD1LG2 mRNA- 9p24.1/9p24.1 intra- CD274 encodes for PDCD1LG2 encodes for KIAA1432/PDCD1 no mRNA chromosomal programmed death ligand programmed cell death 1 LG2 1, PD-L1, an immune ligand 2, PD-L2 inhibitory receptor ligand that is expressed by hematopoietic and non- hematopoietic cells, such as T cells and B cells and various types of tumor cells. MUSK/LPAR1 mRNA- 9q31.3/9q31.3 intra- MUSK encodes a muscle- LPAR1 encodes for a NAA15/LPAR1; no mRNA chromosomal specific tyrosine kinase lysophosphatidic acid SNX30/LPAR1 receptor. The encoded (LPA) receptor from a protein may play a role in group known as EDG clustering of the receptors that mediate acetylcholine receptor diverse biologic functions, including proliferation, platelet aggregation, smooth muscle contraction, inhibition of neuroblastoma cell differentiation, 26 chemotaxis, and tumor cell invasion. DLG2/PICALM mRNA- 11q14.1/11q14.2 intra- DLG2 encodes for discs PICALM encodes for LRP5/DLG2; no mRNA chromosomal large MAGUK scaffold phosphatidylinositol ARRB1/DLG2; protein 2, a member of the binding clathrin assembly INPPSA/DLG2: membrane-associated protein that may be PLXNB2/DLG2: guanylate kinase required to determine the PICALM/RP11- (MAGUK) family. The amount of membrane to 849H4.2; encoded protein forms a be recycled, possibly by PICALM/MLLT10; heterodimer with a related regulating the size of the MLLT10/PICALM; family member that may clathrin cage. ARRB1/PICALM interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins NUMA1/GRIA3 mRNA- 11q13.4/Xq25 inter- NUMA1encodes for a GRIA3 encodes for NUMA1/FAM83B; NUMA1/SFN mRNA chromosomal large protein interacting glutamate ionotropic NUMA1/ADARB2; translocation with microtubules and receptor AMPA type NUMA1/PTH; playing a role in the subunit 3. The subunit NUMA1/AATF; formation and organization encoded by this gene NUMA1/PIPTNM1; of the mitotic spindle belongs to a family of NUMA1/PPP2R5B; during cell division. AMPA (alpha-amino-3- NUMA1/IQSEC3; hydroxy-5-methyl-4- NUMA1/TRPT1; isoxazole propionate)- NUMA1/ADHB12; sensitive glutamate NUMA1/CRYM; receptors, and is subject NUMA1/CCT5; to RNA editing (AGA- SHANK2/NUMA1; >GGA; R->G). STAG2/GRIA3 PPP6R3/MLL mRNA- 11q13.2/11q23.3 intra- SAPS3 encodes for the MLL,also known as PPP6R3/YAP1; no mRNA chromosomal phosphatase regulatory KMT2A lysine PPP6R3/POLD3; subunit 3 that modulates methyltransferase, PPP6R3/SSH2; the activity of phosphatase- encodes a transcriptional PPP6R3/FADD; 6 catalytic subunit by coactivator that plays an PPP6R3/SPTBN3; restricting substrate essential role in regulating PPP6R3/MTL5; specificity, recruiting gene expression during PPP6R3/LRP5; substrates, and determining early development and PPP6R3/ARHGAP1 the intracellular hematopoiesis. RNF121/PPP6R3; localization of the KDM2A/PPP6R3; holoenzyme. STRN3/PPP6R3; PC/PPP6R3; RAB11A/PPP6R3; CCDC132/PPP6R3; 27 MLL/ATP5L; MLL/SLC22A10; MLL/CD86; MLL/MLLT10; MLL/ELL; MLL/MLLT4; MLL/MLLT3; MLL/IGHMBP2: MLL/FYN; MLL/ZDHHC7; MLLT4/MLL; ENSG000002311 lncRNA- 12/12q21.2 intra- lnc-NAV3 NAV3 belongs to the CPSF6/NAV3; no 21/NAV3 mRNA chromosomal neuron navigator family PDK3/NAV3 and is expressed predominantly in the nervous system. The encoded protein contains coiled-coil domains and a conserved AAA domain characteristic for ATPases associated with a variety of cellular activities. ZMYM2/TRIM28 mRNA- 13q12.11/19q13.4 inter- ZMYM2 encodes for zinc TRIM28 encodes ZMYM2/MTMR6; no mRNA 3 chromosomal finger MYM-type tripartite motif containing ZMYM2/KIAA0564; translocation containing 2, also named 28 protein that mediates ZMYM2/DMRT2; ZNF118 that may act as a transcriptional control by TRIM28/ZBTB45 transcription facto and be interaction with the part of a BHC histone Kruppel-associated box deacetylase complex. repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. TRAF3/ENSG000 mRNA- 14q32.32/14 intra- TRAF3 encodes for TNF long intergenic non- TRAF3/MYO16; TRAF3/CDC42 00259717 lncRNA chromosomal receptor associated factor 3, protein coding RNA 677 TRAF3/RCOR1; BPB a member of the TNF TRAF3/SFXN1; receptor associated factor TRAF3/BMP3; (TRAF) protein family. TRAF3/WDR20; TRAF proteins associate SLC22A23/TRAF3; with, and mediate the signal transduction from members of the TNF receptor (TNFR) 28 superfamily. This protein participates in the signal transduction of CD40, a TNFR family member important for the activation of the immune response. ENSG000002594 lncRNA- 15/15q13.3-q14 intra- intergenic lncRNA (lnc- The protein encoded by RYR3/LARP4; no 46/RYR3 mRNA chromosomal FMN1-4) this gene is a ryanodine RYR3/BUB1B; receptor, which functions LARP4/RYR3 to release calcium from intracellular storage for use in many cellular processes. WDR90/RHOT2 mRNA- 16p13.3/16p13.3 intra- WDR90 encodes for WD This gene encodes a WDR90/RAB40C; no mRNA chromosomal repeat domain 90 whose member of the Rho family KIAA1731/WDR90 function in humans
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