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A Comprehensive Approach Characterizing Fusion Proteins And Supplementary Data A Comprehensive Approach Characterizing Fusion Proteins and Their Interactions Using Biomedical Literature Somnath Tagore1, Alessandro Gorohovski1, Lars Juhl Jensen2 and Milana Frenkel-Morgenstern1* 1 The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, Safed 13195, ISRAEL 2 Cellular Network Biology Group, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK *[email protected] 1. Table S1: Root and relation tokens, Bibliography 2. Table S2: Action Tokens for Fusion PPI 3. Table S3: Synonyms for Fusions, Dictionary 4. Table S4: Rulebase 5. Table S5: Fusion tokens identified by ProtFus for 100 PubMed IDs 6. Table S6: Fusion PPIs tokens identified by ProtFus for 100 PubMed IDs Table S1: Root and relation tokens, Bibliography Root token Relation tokens activate activates, activating, activator block blocks, blocking, blocked, blocks in, blocks with chimera chimeric, chimeric gene, chimeric genes, chimeric transcript depend dependent, depends on, depends to, depending on domain domains express expression, expressed in, expressed with, expresses in family fusions, fusion transcript, fusion transcripts, fusion protein, fusion proteins, fusion fusion gene, fusion genes gene genes, gene fusion interaction interactions, interactions with protein proteins reduce reduced, reduced form residue residues transcript transcripts Table S2: Action Tokens for Fusion PPI Root token Relation tokens Abolish abolish, abolishes, abolished, abolishing Accelerate accelerate, accelerates, accelerated, accelerating Acceptor acceptor Accumulate accumulate, accumulates, accumulated, accumulating, accumulation Acetylate acetylate, acetylates, acetylated, acetylating, acetylation Activate activate, activates, activiated, activating, activation, activator Affect affect, affects, affected, affecting Alter alter, alters, altered, altering, alteration Amplify amplify, amplifies, amplified, amplifying, amplification Apoptosis apoptosis Assemble assemble, assembles, assembled, assembling Associate associate, associates, associated, associating, association Attach attach, attaches, attached, attaching, attachment Attack attack, attacks, attacked, attacking Bind bind, binds, bound, binding Block block, blocks, blocked, blocking carbamoylate, carbamoylates, carbamoylated, carbamoylating, Carbamoylate carbamoylation Carboxylate carboxylate, carboxylates, carboxylated, carboxylating, carboxylation Catalyze catalyze, catalyzes, catalyzed, catalyzing Cleave cleave, cleaves, cleaved, cleaving Co- immunoprecipitat co-immunoprecipitate, co-immunoprecipitates, co-immunoprecipitated, co- e immunoprecipitating, co-immunoprecipitation, co-immunoprecipitations Compare compared, comparison, compared to Complex complex, complexes, complexed, complexing, complexation Conjugate conjugate, conjugates, conjugated, conjugating, conjugation Contact contact, contacts, contacted, contacting Couple coupled, coupled with, coupled to Covalent covalent link, covalently linked to Deaccetylate deaccetylate, deaccetyltes, deaccetylated, deaccetylating, deaccetylation Deaminate deaminate, deaminates, deaminated, deaminating, deamination decarboxylate, decarboxylates, decarboxylated, decarboxylating, Decarboxylate decarboxylation Decrease decrease, decreases, decreased, decreasing Dehydrate dehydrate, dehydrates, dehydrated, dehydrating, dehydration dehydrogenate, dehydrogenates, dehydrogenated, dehydrogenating, Dehydrogenate dehydrogenation Demethylate demethylate, demethylates, demethylated, demethylating, demethylation dephosphorylate, dephosphorylates, dephosphorylated, dephosphorylating, Dephosphorylate dephosphorylation Deplete deplete, depletes, depleted, depleting, depletion Disassemble disassemble, disassembles, disassembled, disassembling Discharge discharge, discharges, discharged, discharging Dock dock, docks, docked, docking down-regulate, down-regulates, down-regulated, down-regulating, down- Down-regulate regulation downregulate, downregulates, downregulated, downregulating, Downregulate downregulation Elevate elevate, elevates, elevated, elevating, elevation Enhance enhance, enhances, enhanced, enhancing Express express, expresses, expressed, expressing, expression, express as Formylate formylate, formylates, formylated, formylating, formylation Fusion fusions, fusion proteins Glycosylate glycosylate, glycosylates, glycosylated, glycosylating, glycosylation Hasten hasten, hastenes, hastening, hastened heterodimerize, heterodimerizes, heterodimerizing, heterodimerized, Heterodimerize heterodimerization, heterodimer, heterodimers homodimerize, homodimerizes, homodimerizing, homodimerized, Homodimerize homodimerization, homodimer, homodimers hydrolyse hydrolyse, hydrolyses, hydrolysing, hydrolysed, hydrolysis Inactivate inactivate, inactivates, inactivated, inactivating, inactivation Incite incite, incites, incited, inciting Induce induce, induces, induced, inducing, induction Infect infect, infects, infected, infecting Influence influence, influences, influencing, influenced Inhibit inhibit, inhibits, inhibited, inhibiting, inhibition, inhibitors Initiate initiate, initiates, initiated, initiating, initiation Interact interact, interacts, interacts, interacting, interaction Impair impair, impairs, impaired, impairing Isomerize isomerize, isomerizes, isomerized, isomerizing, isomerization Ligate ligate, ligates, ligated, ligating, ligation, ligand Mediate mediate, mediates, mediated, mediating Methylate methylate, methylates, methylated, methylating, methylation Modify modify, modifies, modified, modifying, modification Modulate modulate, modulates, modulating, modulated Myogenesis myogenesis Overexpress overexpress, overexpresses, overexpressed, overexpressing, overexpression Oxidize oxidize, oxidizes, oxidized, oxidizing, oxidation Pair pair, pairs, paired, paring Participate participate, participates, participated, participating, participation Peroxidize peroxidize, peroxidizes, peroxidized, peroxidizing, peroxidation phosphorylate, phosphorylates, phosphorylated, phosphorylating, Phosphorylate phosphorylation Prevent prevent, prevents, prevented, preventing Produce produce, produces, produced, producing, production Promote promote, promotes, promoted, promoting, promotion Protein proteins, protein-protein, PPI React react, reacts, reacted, reacting, reaction Recognize recognize, recognizes, recognized, recognizing, recognition Recruit recruit, recruits, recruited, recruiting Regulate regulate, regulates, regulated, regulating, regulation Replace replace, replaces, replaced, replacing Repress repress, represses, repressed, repressing, repression Severe severe, severes, severed, severing Split splitting Stimulate stimulate, stimulates, stimulated, stimulating, stimulation, stimulator Substitute substitute, substitutes, substituted, substituting, substitution Suppress suppress, suppresses, suppressed, suppressing, suppression Tether Tether, tethers, tethered, tethering transactivate, transactivates, transactivated, transactivating, transactivation, Transactivate transactivator Transaminate transaminate, transaminates, transaminated, transaminating, transamination Ubiquitinate ubiquitinate, ubiquitinates, ubiquitinated, ubiquitinating, ubiquitination Upregulate upregulate, upregulates, upregulated, upregulating, upregulation, upregulator up-regulate, up-regulates, up-regulated, up-regulating, up-regulation, up- Up-regulate regulator Table S3: Synonyms for Fusions, Dictionary Alternate Fusion proteins Synonyms representations ews fli1, EWSR1 EWS, SH2D1B EAT2 , ELK1, PDGFC SCDGF, ETV2 EWSR1/FLI1, EWS-FLI1 ER71,ETSRP71 EWS FLI-1 Fc-containing NA NA motif-GST NA NA EPO-Fc NA NA VpHsf-GFP NA NA GLP-1 NA NA GLP-1 NA NA GFP-SlGGB1 NA NA receptor-Fc NA NA LSL-tagged NA NA LSL-tagged NA NA Ag85B-ESAT6 NA NA Rep/VP rep VP0041, rep VP02_18990 Rep-VP Rep/VP NA NA NS1-epitope NA NA DISC1-Boymaw NA NA DISC1-Boymaw NA NA RUNX1 AML1,CBFA2, RUNX1T1 AML1T1,CBFA2T1,CDR,ETO,MTG8, TCF12 BHLHB20,HEB,HTF4, SON C21orf50,DBP5,KIAA1019,NREBP,HSPC310, CBFA2T3 AML1/ETO MTG16,MTGR2,ZMYND4 AML1-ETO AcrB-AcrA NA NA Antibody- cytokine NA NA SRRP1-GFP NA NA E3-ubiquitin NA NA PD-LIg NA NA PD-L1Ig NA NA receptor-Fc NA NA ZC3HC1 NIPA,HSPC216, PPID CYP40,CYPD, SFPQ NPM-ALK PSF NPM/ALK GluA2-GluK NA NA F-specific NA NA HN-specific NA NA His-SUMO NA NA VP2-VP3 NA NA VP2-VP3 NA NA his-tag NA NA TMPRSS2-ERG ERG TMPRSS2/ERG RET CDHF12,CDHR16,PTC,RET51, TRIM24 RNF82,TIF1,TIF1A, TRIM33 KIAA1113,RFG7,TIF1G, NCOA4 ARA70,ELE1,RFG, MAPK15 ERK7,ERK8, SH2B1 KIAA1299,SH2B, PDLIM7 ENIGMA, RET- RET/PTC2, RET/PTC ELE1, ELE1-RET RET-PTC BMP7-BMP2 BMPR2 PPH1, Bmpr2 BMPP7/BMP2 MAP-1 NA NA PROTEIN-ES1 NA NA RPS6-AtHD2B NA NA thioredoxin- tagged NA NA NKp80-Fc NA NA NKp80-Fc NA NA BCR-ABL1 SETBP1 KIAA0437, BTK, Bach2, ZNFN1A1 IKZF1, BCR/ABL1 BCR-ABL1 NA NA Vpr-IN vpr, VPRBP DCAF1,KIAA0800,RIP, Vpr/IN protein-NCX1 NA NA hepcidin- thioredoxin NA NA EML1 EMAP1,EMAPL,EMAPL1, EML2 EML4-ALK EMAP2,EMAPL2 EML4/ALK NAB2-STAT6 NA NA NAB2-STAT6 NA NA NAB2-STAT6 NA NA NAB2-STAT6 NA NA LDHC-RFP NA NA protein- nitroreductase NA NA antibody/Fc NA NA BCR-ABL NA NA catalase- lipoxygenase NA NA catalase- lipoxygenase NA NA KIR-Fc NA NA MYB-NFIB MYB/NFIB MYB/NFIB IFNalpha1- THYalpha1 NA NA poIFNalpha1- THYalpha1 NA NA poIFNalpha1- THYalpha1 NA NA envelope-NS1 NA NA Flag-tagged NA NA Flag-tagged NA NA MIIA-Strep NA NA hsp70-p24 NA NA EGFP-HttQ52 NA NA AdoMetDC- SpdSyn NA NA protein-tagged NA NA signaling- enhanced NA NA BCR-ABL NA NA CD19-specific NA NA Osteocalcin-
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