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utils_data.py
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dna_marker_genes_melanoma = ["AKT1", "AKT2", "AKT3", "ALK", "CDKN2A", "CDKN2B", "CCND1", "CCND2", "CCND3", "ERBB2", "KDR", "CDK4", "CDK6", "BRAF", "MET", "FGFR1", "FGFR2", "FGFR3", "PTEN", "NF1", "BAP1", "EGFR", "BRCA2", "BRCA1", "KIT", "TP53", "JAK1", "JAK2", "B2M", "MITF", "MAP2K1", "NRAS"]
neutral_clones_melanoma = ['MACEGEJ_2', 'MADIBUG_0', 'MADIBUG_1', 'MAHEFOG_0', 'MAJOFIJ_1', 'MAJOFIJ_2', 'MALYLEJ_0', 'MANOFYB_1', 'MANOFYB_2', 'MAPOXUB_0', 'MATIWAQ_0', 'MEDYCAR_0', 'MEFOCUR_0', 'MEFOCUR_2', 'MEHUFEF_6', 'MEKOBAB_0', 'MELIPIT_2', 'MELIPIT_3', 'MELIPIT_4', 'MELUKUZ_0', 'MEMEMUH_0', 'MEMEMUH_1', 'MEMEMUH_4', 'MENYTEK_0', 'MENYTEK_1', 'MEVIXYV_0', 'MEVIXYV_2', 'MIBAFUK_0', 'MIBAFUK_1', 'MIDEKOG_0', 'MIFIMAB_5', 'MIFOGIL_1', 'MIFOGIL_3', 'MIFOGIL_4', 'MIGEKUT_1', 'MIGEKUT_2', 'MIHIFIB_2', 'MIHIFIB_3', 'MIHIFIB_4', 'MIKYCYN_0', 'MILABYL_0', 'MILABYL_1', 'MILABYL_5', 'MIMANAR_0', 'MIMANAR_2', 'MIMANAR_3', 'MIMANAR_4', 'MIMANAR_5', 'MOCELOJ_4', 'MODUDOL_0', 'MOFYCAG_0', 'MOFYCAG_2', 'MOTAMUH_4', 'MOVAZYQ_5', 'MUGAKOL_5', 'MUJAGIF_0', 'MUJAGIF_5', 'MUKAGOX_4', 'MULYMUP_0', 'MUMIFAD_0', 'MYBYHER_0', 'MYBYHER_1', 'MYBYHER_2', 'MAHACEB_0', 'MAHACEB_3', 'MEXUXEH_0', 'MEXUXEH_1', 'MIJUCYK_0', 'MYJILAS_1', 'MYKOKIG_0', 'MACYHYS_0', 'MACYHYS_3', 'MADUBIP_0', 'MADUBIP_1', 'MELYPEB_0', 'MELYPEB_6', 'MIDOBOL_0', 'MIDOBOL_2', 'MISYPUP_0', 'MISYPUP_3', 'MOBUBOT_1', 'MOBUBOT_2', 'MOBUBOT_3', 'MOBUBOT_4', 'MOQAVIJ_0', 'MOQAVIJ_1', 'MUDEFAW_0', 'MUDEFAW_1', 'MUDEFAW_3', 'MECYGYR_0', 'MIKOBID_0', 'MIKOBID_3', 'MUCADOP_0', 'MUCADOP_3', 'MAJEFEV_0', 'MAJEFEV_4', 'MOGYLIP_2', 'MENEMAN_0', 'MYNELIC_0', 'MYNESYB_0', 'MADEGOD_0', 'MADEGOD_5']
samples_to_remove_melanoma = ["MAHOBAM", "MENYTEK", "MEXUXEH", "MIDEKOG", "MADUBIP"]
dna_marker_genes_ovarian = ["ABCB1", "ABL1", "ALCAM", "ALK", "AR", "ARAF", "AREG", "ATM", "AURKA", "BCL2L11", "BRAF", "BRCA1", "BRCA2", "CCND2", "CD274", "CDKN1A", "CHEK2", "CXCR4", "CYP17A1", "DEFA1", "DNMT1", "DNMT3A", "EGFR", "EPHB4", "ERBB2", "ERBB3", "ERCC2", "EREG", "ESR1", "FANCC", "FLT3", "FOXP3", "GNA11", "HSPA5", "IDH1", "IDH2", "KIT", "KRAS", "MDM2", "MEK/ERK", "MET", "MGMT", "MLL", "MMP2", "MMP9", "MRE11", "MTHFR", "MTOR", "NF1", "NF2", "NRAS", "NT5E", "PDCD4", "PDGFB", "PDGFRA", "PDGFRB", "PIK3CA", "PROM1", "PTEN", "RAD51", "RB", "RB1", "RET", "ROS1", "RRM1", "SMAD4", "STMN1", "TIMP1", "TOP2A", "TP53", "TSC1", "TSC2", "VEGFA"]
neutral_clones_ovarian = ['ABABECE_0', 'ABABECE_2', 'ABABECE_4','ADEGAKO_0','AFACYKY_0','AFELOMY_0', 'AFELOMY_2', 'AFELOMY_3', 'AFELOMY_4','AGOMUNI_0', 'AGOMUNI_3','AWITEXO_0', 'AWITEXO_1', 'AWITEXO_2','AWOVAXI_0','OB225_0','OBABACY_0','OCANYTE_3','ODAFUGU_0', 'ODAFUGU_2', 'ODAFUGU_3','ODAMILU_0', 'ODAMILU_4','ODAQUPA_1', 'ODAQUPA_2', 'ODAQUPA_3','ODEGOHY_0','OHACAHY_0', 'OHACAHY_1','OHAMUME_3', 'OHAMUME_5','OHANIQY_2', 'OHANIQY_3', 'OHANIQY_4','OHU1D_0','OKAGOCY_0','OKEBYDA_3','OKEKIDE_0', 'OKEKIDE_1', 'OKEKIDE_2','OLEFUTI_0', 'OLEFUTI_4','OLEKESU_0','OMABOPY_0', 'OMABOPY_2','OMAFYSU_1', 'OMAFYSU_2', 'OMAFYSU_3','OMAJIQI_1', 'OMAJIQI_2','OMAJORO_1','OMEFOMO_1', 'OMEFOMO_3', 'OMEFOMO_4','ONAKERE_0', 'ONAKERE_3','OPAPUHU_0','OQADIRY_0', 'OQADIRY_2','OQADOQU_0', 'OQADOQU_1','OQEFIRU_0', 'OQEFIRU_3','OQEMOGA_0', 'OQEMOGA_2','ORAJIMY_1','ORAVAFU_0','OTAMAZA_0', 'OTAMAZA_1','OTEWUZO_0', 'OTEWUZO_1', 'OTEWUZO_2','OTX01_0','OVAMUZI_0','OXEXYCY_1', 'OXEXYCY_2', 'OXEXYCY_3','OXUMUZU_0', 'OXUMUZU_1', 'OXUMUZU_2','OZ0G5_0', 'OZ0G5_4','OZUVAPU_0','OZQ5C-YRS_0','OBJO4-YRS_4','OBABEBU_0','ONWLE-YR4_0','OKW5U-YRS_0']
samples_to_remove_ovarian = ["ODIDUKU", "OV2NP", "AWAREZA", "AXIPIDE", "OCAGEHY", "ONAHYPU", "AGORILU", "OGOBIGU", "OVIKYWA", "O46II", "O610T", "O7UW4", "OY3WE", "AWITEXO"]
dna_marker_genes_aml = ['ABL1','ANKRD26','ASXL1','ATRX','BCOR','BCORL1','BRAF','BTK','CALR','CBL','CBLB','CBLC','CCND2','CDC25C','CDKN2A','CEBPA','CSF3R','CUX1','CXCR4','DCK','DDX41','DHX15','DNMT3A','ETNK1','ETV6','EZH2','FBXW7','FLT3','GATA1','GATA2','GNAS','HRAS','IDH1','IDH2','IKZF1','JAK2','JAK3','KDM6A','KIT','KMT2A','KRAS','LUC7L2','MAP2K1','MPL','MYC','MYD88','NF1','NOTCH1','NPM1','NRAS','PDGFRA','PHF6','PPM1D','PTEN','PTPN11','RAD21','RBBP6','RPS14','RUNX1','SETBP1','SF3B1','SH2B3','SLC29A1','SMC1A','SMC3','SRSF2','STAG2','STAT3','TET2','TP53','U2AF1','U2AF2','WT1','XPO1','ZRSR2']
neutral_clones_aml = ['DOROBOF_3','DOROFEG_0', 'DOROFEG_1','DOMIBEG_0', 'DOMIBEG_1', 'DOMIBEG_2','DOPIBOJ_0','DADEDEM_0','DEJAFAB_0','DEJIBEB_0','DYBEKIM_0', 'DYBEKIM_1','DYVUHYB_0','DYWYJUB_0','DOBIFIK_1','DYBAHAK_0','DYBIDYF_0','DEBEGUC_0', 'DEBEGUC_1', 'DEBEGUC_2','DIBAHUC_0','DUBIBEP_0','DOBAFAM_0','DIBADAG_0','DOBEKUF_0', 'DOBEKUF_1','DUBEJIH_0','UGABOLU_0', 'UGABOLU_1','DABIJUH_0','UTAPYSO_3','DEBEDIG_0']
samples_to_remove_aml = ["DADEDEM", "DEBEGUC", "DEJAFAB", "DEJIBEB", "DIBAHUC", "DOBEKUF", "DOMIBEG", "DOPIBOJ", "DOROFEG", "DUBIBEP", "DYBEKIM", "DYVUHYB"]
'''
###################################
scrna_melanoma_signatures_tirosh16 = ["ABCB5", "ACSL3", "ATP1A1", "BIRC7", "CAPN3", "CDH1", "CDH19", "CDK2", "CSPG4", "ERBB3", "FXYD3", "GJB1", "GPM6B", "GPR143", "IGSF8", "LINC00473", "LOXL4", "MAGEA6", "MBP", "MELTF", "MIA", "MITF", "MLANA", "MLPH", "NT5DC3", "PAX3", "PIR", "PLEKHB1", "PLP1", "PMEL", "PRAME", "QDPR", "QPCT", "RAB38", "ROPN1B", "S100A1", "S100B", "SEMA3B", "SERPINA3", "SERPINE2", "SLC24A5", "SLC26A2", "SLC45A2", "SOX10", "ST3GAL4", "ST6GALNAC2", "TYR"]
scrna_melanoma_signatures_literature = ["AQP1", "AXL", "BGN", "CDH13", "CDH2", "CYR6", "EGFR", "FEZ1", "FOSL2", "GFRA2", "GFRA3", "IGFBP6", "L1CAM", "LOXL2", "NGFR", "PDGFRB", "POSTN", "RGS5", "RSPO3", "SLC22A17", "SLC2A1", "SLIT2", "SLITRK6", "SOX9", "TCF4", "TGFBI", "TGM2", "TMEM176B", "TNC", "VIM", "WNT5A"]
###################################
'''