R package for the identification of cancer-associated mutated genes using gene expression and mutation data.
Rabadan R., Mohamedi Y., Rubin U., Chu T., Alghalith A. N., Elliott O., Arnes L., Cal S., Obaya A. J., Levine A. J., and Camara P. G., "Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis". Nature Communications 11 (2020) 3808. DOI: 10.1038/s41467-020-17659-7.
Updates to this tutorial are ongoing. What follows displays a near-complete workflow for using this package.
We will use low grade glioma expression and mutation data to demonstrate
the TDAmut pipeline. The sample data is formatted from publically
available TCGA data and is provided in the TDAmut package. Expression
data is assumed to be normalized data (e.g. (log_2[1+TPM])) formatted
as a matrix (rows = samples, columns = genes). Mutation data is assumed
be in a table organized by Sample, Gene, and Type (e.g. missense,
nonsense, splice, frameshift, …).
The user is afforded several options in each function of TDAmut. We
implemented default options which can be a helpful starting point for
the user.
Install and load TDAmut:
devtools::install_github("CamaraLab/TDA-TCGA")
library(TDAmut)Note that this package requires prior installation of additional packages not available via CRAN (e.g., bioDist from BioConductor, RayleighSelection from the CamaraLab GitHub) in order to succeed. If these packages are not currently available on your system, they will need to be installed prior to installing the TDAmut package.
TDAmut takes as input the gene expression matrix and mutation table of the tumor cohort. The expected format for these two files can be seen in the example
files in the folder data. The first step in the TDAmut pipeline is to create a TDAmut object. The TDAmut object is used as an intermediate across all functions
and holds data and topological representations produced in this pipeline.
exp_data_path <- "data/LGG_Full_TPM_matrix.csv"
mut_data_path <- "data/LGG_Muts.txt"
LGG_object <- create_TDAmut_object(exp_data_path, mut_data_path)## Removed 305 genes with no expression data
## Removed samples in expression data not in mutation data: 'TCGA-DU-7014-01A', 'TCGA-DU-A7TI-01A', 'TCGA-HW-7493-01A', 'TCGA-TQ-A7RK-02B'
## The following genes have mutation data but no expression data. They will not be considered for filtering of negative correlations later in the TDAmut pipeline: 'LEPREL1.55214', 'KRTAP21-2.337978', 'MT-ND4.4538', 'HLA-DRA.3122', 'KAL1.3730', 'MT-ND5.4540', 'MT-CO1.4512', 'MT-CO3.4514', 'ZRSR1.7310', 'C14orf182.283551', 'HLA-DQB2.3120', 'GPR124.25960', 'GPR98.84059', 'KRTAP4-6.81871', 'HLA-DMB.3109', 'OR9G1.390174', 'FSIP2.401024', 'OR2T7.81458', 'FRG1B.284802', 'FRMPD3.84443', 'C12orf36.283422', 'HLA-DQA2.3118', 'NKX2-1.7080', 'KRTAP1-5.83895', 'ANKRD36C.400986', 'MT-CYB.4519', 'HLA-C.3107', 'KRTAP4-11.653240', 'KRTAP17-1.83902', 'CNTNAP3B.728577', 'KIAA1045.23349', 'GCN1L1.10985', 'HLA-F.3134', 'KRTAP4-4.84616', 'KRTAP9-9.81870', 'KRTAP19-1.337882', 'KRTAP10-5.386680', 'KRTAP4-2.85291', 'GPR112.139378', 'KRTAP10-3.386682', 'LPHN3.23284', 'KRTAP13-1.140258', 'KRTAP10-12.386685', 'HLA-A.3105', 'GPR110.266977', 'FAM115C.285966', 'UBBP4.23666', 'NPIPA5.100288332', 'HIST1H4G.8369', 'ZNF812.729648', 'NKX2-2.4821', 'AKR1CL1.340811', 'BAI1.575', 'SLC9B1P1.100128190', 'KRTAP4-8.728224', 'CCDC132.55610', 'EBLN1.340900', 'KRTAP12-4.386684', 'CXorf22.170063', 'GPR115.221393', 'FAM178A.55719', 'GPR125.166647', 'AC073343.1.0', 'C4B.721', 'EMR1.2015', 'WDR16.146845', 'HEATR2.54919', 'NBPF20.100288142', 'MYZAP.100820829', 'OR5H15.403274', 'KRTAP19-2.337969', 'LPHN2.23266', 'CHDC2.286464', 'TTC6.319089', 'KIAA1377.57562', 'ERO1LB.56605', 'MUC5AC.4586', 'KRTAP4-9.100132386', 'OR1D5.8386', 'KIAA1279.26128', 'SMEK1.55671', 'GPR111.222611', 'KIAA1244.57221', 'ZNF852.285346', 'C17orf70.80233', 'KRTAP10-10.353333', 'LEPRE1.64175', 'C1orf86.199990', 'KRTAP4-7.100132476', 'FAM154B.283726', 'FPGT-TNNI3K.100526835', 'GPR116.221395', 'DAK.26007', 'GPR128.84873', 'OTOGL.283310', 'EMR2.30817', 'HLA-DPB1.3115', 'LOC101929950.101929950', 'KRTAP5-2.440021', 'PCDHB17.54661', 'PLA2G4B.100137049', 'NHP2L1.4809', 'TMEM189-UBE2V1.387522', 'ANKRD32.84250', 'GPR113.165082', 'HLA-DMA.3108', 'KRTAP4-3.85290', 'GPR97.222487', 'C6orf211.79624', 'TSSK2.23617', 'C7orf55-LUC7L2.100996928', 'LPHN1.22859', 'MUC3A.4584', 'TENC1.23371', 'HLA-E.3133', 'CCDC180.100499483', 'HLA-DRB1.3123', 'FAM154A.158297', 'GPR133.283383', 'B3GALTL.145173', 'GPR126.57211', 'PTPLAD2.401494', 'KRTAP5-4.387267', 'GPR64.10149', 'KRBOX1.100506243', 'RP11-467N20.5.0', 'CCL4L1.9560', 'PTGES3L.100885848', 'C5orf55.116349', 'TMEM194A.23306', 'SMEK2.57223', 'KRTAP10-7.386675', 'KRTAP9-8.83901', 'KRTAP1-1.81851', 'KRTAP9-2.83899', 'DEFA3.1668', 'KRTAP10-6.386674', 'ZFYVE20.64145', 'AGAP10.728127', 'KRTAP5-3.387266', 'IQCJ-SCHIP1.100505385', 'PRAMEF7.441871', 'HIST1H2AA.221613', 'KRTAP9-1.728318', 'ERO1L.30001', 'TCEB3CL2.100506888', 'IGJ.3512', 'KRTAP10-2.386679', 'ZNF724P.440519', 'FOLR4.390243', 'TMEM256-PLSCR3.100529211', 'ZNF587B.100293516', 'TRIM49C.642612', 'DEFB113.245927', 'KRTAP5-1.387264', 'EMR3.84658', 'KRTAP10-1.386677', 'NCBP2L.392517', 'NKX3-1.4824', 'NPIPB4.440345', 'OR5I1.10798', 'RP11-166B2.1.0', 'NMS.129521', 'KRTAP5-8.57830', 'NPIPA8.101059953', 'GOLGA6L2.283685', 'CD97.976', 'KRTAP10-8.386681', 'RNF223.401934', 'C2orf43.60526', 'MT-CO2.4513', 'ELTD1.64123', 'ERVW-1.30816', 'HLA-DOA.3111', 'RBAK-RBAKDN.100533952', 'GOLGA8I.283796', 'ZNF783.100289678', 'UGT2B17.7367', 'HLA-DRB5.3127', 'KRTAP20-2.337976', 'NPIPB11.728888', 'GOLGA6L3.100133220', 'KRTAP21-1.337977', 'OPN1MW2.728458', 'KRTAP4-5.85289', 'WASH4P.374677', 'ZNF728.388523', 'FAM47E-STBD1.100631383', 'TRIM73.375593', 'OR52B1P.81274', 'IGHV3OR16-9.28307', 'MTPN.136319', 'RBMY1E.378950', 'NUTM2E.283008', 'MS4A4E.643680', 'OR4C5.79346', 'OR14K1.343170', 'HLA-DQA1.3117', 'CT47A6.728062', 'KRTAP5-5.439915', 'C11orf72.100505621', 'KRTAP10-9.386676', 'KRTAP11-1.337880', 'RP11-146E13.4.0', 'TRAV9-2.28677', 'OTX2-AS1.100309464', 'LINC00969.440993', 'MT-ND2.4536', 'KRTAP9-3.83900', 'HLA-DRB6.3128', 'DAOA-AS1.282706', 'DNM1P47.100216544', 'RP11-423O2.5.0', 'LOC728339.728339', 'RP11-254I22.1.0', 'SNHG24.101929369', 'LINC00854.100874261', 'LOC727993.727993', 'MIR646HG.284757', 'AC027612.3.0', 'LOC63930.63930', 'IGHG1.3500', 'TUBB8P7.197331', 'MIR146A.406938', 'RP11-308D16.4.0', 'CTC-535M15.2.0', 'CCDC175.729665', 'TRGC2.6967', 'IGHA1.3493', 'KRT17P2.339241', 'RP11-739N20.2.0', 'RP11-686D16.1.0', 'OVOS2.144203', 'RP11-847H18.2.0', 'GOLGA6L17P.642402', 'SNHG14.104472715', 'LOC101928372.101928372', 'LOC400800.400800', 'FLJ16171.441116', 'NOS2P1.645740', 'SOX9-AS1.400618', 'SLC9A7P1.121456', 'TRAV8-2.28684', 'NANOGP1.404635', 'LOC101927905.101927905', 'IGLV3-12.28802', 'BAI3.577', 'HERC2P3.283755', 'KRT19P2.160313', 'LOC101927533.101927533', 'MIR381HG.378881', 'RP11-156P1.3.0', 'LINC00971.440970', 'TAPT1-AS1.202020', 'IGHV1OR16-3.28313', 'NUTM2B-AS1.101060691', 'HLA-V.352962', 'KIZ-AS1.101929591', 'IGHV4-28.28400', 'RP11-89K10.1.0', 'IGHV3-33.28434', 'RP11-1028N23.4.0', 'AC015849.16.0', 'RP11-625I7.1.0', 'ZNF503-AS1.253264', 'GNAS-AS1.149775', 'IGHD.3495', 'RP11-149P24.1.0', 'RP11-221N13.4.0', 'IGKV3D-20.28874', 'LINC00987.100499405', 'APCDD1L-AS1.149773', 'LLNLF-65H9.1.0', 'RP11-464F9.1.0', 'LINC00477.144360', 'RP11-807H22.7.0', 'RP11-122F24.1.0', 'ROCK1P1.727758', 'WASH6P.653440', 'RPL12P38.645688', 'BCRP2.400892', 'RP11-85G18.6.0', 'HNRNPKP3.399881', 'RP11-556I14.1.0', 'ZNRD1-AS1.80862', 'IGLV2-28.28812', 'MIR3687-2.103504728', 'LOC101927209.101927209', 'RP11-435B5.5.0', 'LOC101927755.101927755', 'MED15P9.285103', 'LOC403323.403323', 'GAPDHP15.642317', 'HCG17.414778', 'IGHG3.3502', 'H3F3AP4.440926', 'LOC101927079.101927079', 'RP11-504G3.4.0', 'RP11-252A24.2.0', 'UPF3AP2.147150', 'MRPS31P5.100887750', 'IGHG4.3503', 'CTB-134H23.3.0', 'HERC2P9.440248', 'IGLC3.3539', 'TRBV6-8.28599', 'TRBV5-4.28611', 'PBX2P1.5088', 'EIF4E2P2.645207', 'TRDV2.28517', 'UBA6-AS1.550112', 'LOC442028.442028', 'CCT6P3.643180', 'RP11-24M17.5.0', 'KTN1-AS1.100129075', 'LOC100288069.100288069', 'CTD-2251F13.1.0', 'RP11-433J8.2.0', 'MIR371B.100616185', 'LOC105371814.105371814', 'CTC-548K16.2.0', 'NDUFA6-AS1.100132273', 'CTC-260E6.6.0', 'LOC643201.643201', 'TBC1D3P3.653017', 'LRRC37A11P.342666', 'AC016995.3.0', 'KANTR.102723508', 'DPPA3P2.400206', 'RP11-44F14.1.0', 'ANKRD20A5P.440482', 'RP11-114H23.1.0', 'RP11-652G5.1.0', 'RP11-404F10.2.0', 'TRBV29-1.28558', 'IGHV1-18.28468', 'CTB-161M19.4.0', 'INTS4L2.644619', 'RP11-597A11.6.0', 'IGLV7-43.28776', 'TRBV6-7.28600', 'SRGAP2-AS1.100873165', 'IGHV3-38.28429', 'TRAV24.28659', 'SRGAP2B.647135', 'IGHV1-58.28464', 'RP5-991G20.1.0', 'XXbac-BPG308J9.3.0', 'IGHE.3497', 'RP11-324C10.1.0', 'IGHV3-11.28450', 'IGHV3-20.28445', 'RP11-608O21.1.0', 'GPR123.84435', 'RP11-782C8.1.0', 'TRBV19.28568', 'IGHV4OR15-8.28317', 'IGHV3-49.28423', 'MIR377.494326', 'TRAJ57.28698', 'GPR56.9289', 'TRAV41.28640', 'SPINT4.391253', 'SNORD113-3.767563', 'MIR181A1.406995', 'TRAV27.28655', 'MAP3K14-AS1.100133991', 'MIR506.574511', 'TP73-AS1.57212', 'TRIM51HP.440041', 'IGLV2-23.28813', 'C20orf166-AS1.253868', 'IGHV3-72.28410', 'IGHV7-81.28378', 'MIR101-1.406893', 'TRBV4-1.28617', 'MIR380.494329', 'EMR4P.326342', 'IGKV6D-21.28870', 'SNORD114-31.767612', 'MIR518F.574472', 'TRBV6-5.28602', 'IGHV5-51.28388', 'TRBV6-1.28606', 'MIR518A1.574488', 'KRTAP9-4.85280', 'TRAV38-2DV8.28643', 'IGLV8-61.28774', 'IGKV3-20.28912', 'ATF4P4.100127952', 'IGHV3OR15-7.28318', 'HLA-B.3106', 'KIAA1598.57698', 'KRT16P2.400578', 'TRAV17.28666', 'MIR519A2.574500', 'HLA-F-AS1.285830', 'TRDJ1.28522', 'LEPREL2.10536', 'RPLP0P6.220717', 'PCDHB18.54660', 'IGLV3-16.28799', 'ZNF271.10778', 'TRBV11-1.28582', 'KRTAP5-9.3846', 'IGLV2-14.28815', 'TRBC2.28638', 'BAI2.576', 'IGKJ5.28946', 'RP11-337C18.8.0', 'FAIM3.9214', 'FAM21EP.100421577', 'IGHV1-45.28466', 'MIR509-1.574514', 'TRAV26-1.28657', 'IGHV1-24.28467', 'IGHV4-59.28392', 'MIR96.407053', 'IGHG2.3501', 'IGKV1-12.28940', 'LINC00842.643650', 'LRRC53.100144878', 'IGLV6-57.28778', 'BGLT3.103344929', 'TRAV18.28665', 'MIR517A.574479', 'CHEK2P2.646096', 'TRGV9.6983', 'TRDC.28526', 'MIR548A1.693125', 'IGLV11-55.28770', 'TRAV3.28690', 'TBC1D3P5.440419', 'TRGC1.6966', 'PPP1R2P1.100507444', 'IGLV2-18.28814', 'TRBV5-1.28614', 'RP11-156P1.2.0', 'IGLV4-3.28786', 'MIR450A1.554214', 'LOC100507291.100507291', 'LOC101927126.101927126', 'RP11-399K21.11.0', 'TRAV21.28662', 'LINC01500.102723742', 'RP11-439I14.2.0', 'TRBV7-6.28592', 'IGLV5-37.28783', 'TRBV6-6.28601', 'PDPK2P.653650', 'RP11-353N4.5.0', 'GLUD1P2.100381203', 'RP11-67H24.2.0', 'RP13-329D4.3.0', 'KRTAP12-2.353323', 'RP11-271K11.5.0', 'LA16c-23H5.4.0', 'IL9RP3.729486', 'MT1HL1.645745', 'MIR548I2.100302277', 'ZNRF2P2.100271874', 'FAM66B.100128890', 'IGLV1-40.28825', 'HIST2H2BB.338391', 'IGHV3-64.28414', 'LINC00639.283547', 'NUP210P1.255330', 'KRTAP15-1.254950', 'BNIP3P1.319138', 'AC005013.5.0', 'STARD7-AS1.285033', 'AC009120.6.0', 'KRTAP12-1.353332', 'LINC00886.730091', 'KRTAP5-11.440051', 'LOC100130700.100130700', 'TRBV10-2.28584', 'IGLV7-46.28775', 'MIR30B.407030', 'SPACA6P-AS.102238594', 'LINC01597.400841', 'RP11-991C1.2.0', 'RNA5-8SP6.100873336', 'IGLV3-25.28793', 'IGHV3-30.28439', 'LOC101926911.101926911', 'TRBV10-1.28585', 'BSNDP4.106481726', 'NKX2-8.26257', 'AL132989.1.0', 'MIR297.100126354', 'GPR42.2866', 'IGLV3-22.28795', 'AP001347.6.0', 'RP11-159L20.2.0', 'IGHV3-43.28426', 'LINCMD1.101154644', 'RP11-13J8.1.0', 'LRRC37A5P.652972', 'RP11-21G20.3.0', 'ACN9.57001', 'RP11-377D9.3.0', 'ZNF528-AS1.102724105', 'RP11-344E13.3.0', 'MIR517C.574492', 'MTHFD2P1.100287639', 'LOC101927460.101927460', 'LOC101926941.101926941', 'LINC01158.100506421', 'LRCOL1.100507055', 'KRTAP5-10.387273', 'PROX1-AS1.100505832', 'ZNF730.100129543', 'TPTE2P2.644623', 'MIR9-2.407047', 'RP11-340I6.7.0', 'RASA4B.100271927', 'LOC100506457.100506457', 'LOC105373525.105373525', 'CTD-2185K10.1.0', 'CTC-436P18.1.101928630', 'RP11-239H6.2.0', 'RP3-428L16.1.0', 'RP11-27P7.1.0', 'KB-1615E4.2.0', 'KB-1507C5.4.0', 'RP11-1113L8.1.0', 'LOC440446.440446', 'LINC01476.101927728', 'LINC00229.414351', 'LOC101928627.101928627', 'MIR337.442905', 'RP1-241P17.4.0', 'TRBV11-2.28581', 'RP11-640M9.2.0', 'CTD-2296D1.4.0', 'IGHV1OR15-9.390531', 'RP11-51L5.5.0', 'IGHV3-48.28424', 'LOC101928663.101928663', 'RP11-114H24.4.0', 'RP11-478C19.2.0', 'MIR892A.100126342', 'LOC400867.400867', 'LOC283683.283683', 'GS1-124K5.2.0', 'AZGP1P1.646282', 'LINC01359.101927084', 'LOC101927237.101927237', 'LOC101927708.101927708', 'AC073321.4.0', 'MIR663AHG.284801', 'RP11-597A11.1.0', 'IGKV1-6.28943', 'MIR7162.102466227', 'KRTAP10-11.386678', 'RP11-1082L8.3.0', 'RPL34-AS1.285456', 'RP11-526A4.1.0', 'CCNB3P1.100131678', 'RP11-436D23.1.0', 'RP11-314D7.1.0', 'LOC101243545.101243545', 'LOC100507377.100507377', 'TRGV4.6977', 'CTC-512J12.4.0', 'AC018359.1.0', 'CTD-2269F5.1.0', 'KRT223P.643115', 'MIR520E.574461', 'AC007251.2.0', 'RP11-390F4.6.0', 'AC012322.1.0', 'RP11-483E23.2.0', 'RNA5-8SP2.100873571', 'HLA-DOB.3112', 'MIR522.574495', 'PTPLAD1.51495', 'SMURF2P1.0', 'NPIPB1P.729602', 'DNM1P34.729809', 'TRBV7-3.28595', 'LINC00202-2.731789', 'KRT16P6.353194', 'IGKV5-2.28907', 'LINC01378.103689918', 'SUDS3P1.285647', 'GOLGA2P9.440518', 'IL12A-AS1.101928376', 'CYP21A1P.1590', 'LOC101927648.101927648', 'RP11-19N8.4.0', 'C1orf85.112770', 'LINC01239.441389', 'IGLV1-50.28821', 'AP001604.3.0', 'OR10J8P.343409', 'RP11-178C3.1.0', 'LINC01250.101927554', 'HSPD1P6.645548', 'IGHV2-26.28455', 'LINC01122.400955', 'LINC01229.101928248', 'RP11-493L12.5.0', 'LINC00499.100874047', 'LINC00621.100996930', 'IGKV1D-17.28900', 'LIPE-AS1.100996307', 'SMPD4P1.645280', 'LOC101928553.101928553', 'LOC100507053.100507053', 'OR8G1.26494', 'TRGV3.6976', 'SLC2A1-AS1.440584', 'KRTAP19-8.728299', 'PINLYP.390940', 'SMG1P7.100506060', 'LOC101927575.101927575', 'RP11-274B21.1.0', 'MEF2C-AS1.101929423', 'DUXAP8.503637', 'LINC01269.103695436', 'LOC101927040.101927040', 'TRDV1.28518', 'TRBV6-4.28603', 'SNHG23.100507242', 'CTC-338M12.9.0', 'CTD-2184D3.5.0', 'FAM74A7.100996582', 'SNORD3C.780853', 'LOC728715.728715', 'ANKRD30BP3.338579', 'RP11-93K22.13.0', 'CTC-439O9.3.0', 'LOC101928880.101928880', 'TRBV7-1.28597', 'RP11-1166P10.6.0', 'RP1-167F1.2.0', 'LOC101928940.101928940', 'RP11-25I15.2.0', 'LOC100289333.100289333', 'RP11-180I4.2.0', 'IGLV5-45.28781', 'IGHD3-10.28499', 'GOLGA6L7P.728310', 'IGHV3-13.28449', 'SNAP25-AS1.100131208', 'IGHV4-61.28391', 'IGHV3OR16-8.388255', 'CSAG4.100130935', 'RP11-418J17.3.0', 'CTD-2377D24.8.0', 'LOC101929350.101929350', 'KRTAP13-3.337960', 'IGKV6D-41.28869', 'GRIFIN.402635', 'SDCCAG3P1.388478', 'RP5-963E22.4.0', 'LOC101929066.101929066', 'CTD-2066L21.3.0', 'CTD-3092A11.1.0', 'SRP54-AS1.100506157', 'ANKRD20A2.441430', 'LOC100505782.100505782', 'USP32P3.347716', 'IGHV3-53.28420', 'STEAP2-AS1.100874100', 'LINC00674.100499466', 'IGHA2.3494', 'CTD-2245F17.3.0', 'IGHM.3507', 'LOC100420587.100420587', 'LOC642426.642426', 'NKX3-2.579', 'SVILP1.645954', 'LOC100287072.100287072', 'INTS4L1.285905', 'RP11-451O13.1.0', 'RP11-383M4.6.0', 'QRSL1P2.100422330', 'RP11-481J13.1.0', 'TRGV2.6974', 'IGKV1D-16.28901', 'RP11-586K2.1.0', 'SORD2P.653381', 'RP11-645C24.5.0', 'TRAV12-2.28673', 'RP13-228J13.1.0', 'SDAD1P1.157489', 'IGHV1OR16-2.28314', 'AC006988.1.0', 'ISX-AS1.101926957', 'RP11-587D21.4.0', 'LINC01317.104355287', 'LINC00459.100874180', 'IGKV1D-12.28903', 'LINC00202-1.387644', 'TRBV3-1.28619', 'MIR34A.407040', 'RP11-170M17.1.0', 'TRAV7.28686', 'IGHV3-21.28444', 'CYP4F24P.388514', 'TBC1D27.96597', 'LINC00359.100887754', 'LINCR-0001.101929191', 'NIFKP6.100132796', 'CTC-559E9.6.0', 'CTC-513N18.6.0', 'RP11-20E24.1.0', 'TRAJ24.28731', 'ANKRD20A18P.391269', 'LINC00877.285286', 'RP11-161I6.2.0', 'MIR494.574452', 'IGKV1D-8.28904', 'RP11-782C8.2.0', 'AC002331.1.0', 'RP11-796E2.4.0', 'AC005077.5.0', 'FAM177A1P1.728710', 'LOC101928782.101928782', 'MIR24-2.407013', 'MIR940.100126328', 'LOC100289656.100289656', 'EMC3-AS1.442075', 'RP11-431K24.1.0', 'IGHJ6.28475', 'RP11-525A16.4.0', 'MT-ND6.4541', 'IGHV1-46.28465', 'LINC01076.106144602', 'LL22NC03-86D4.1.105373010', 'KRTAP5-6.440023', 'IGHV3-16.28447', 'RP11-509A17.3.0', 'AP000320.7.0', 'RP11-519G16.3.0', 'ERICH1-AS1.619343', 'CTB-35F21.1.0', 'RP5-905H7.3.0', 'SNORD3B-1.26851', 'TRBV9.28586', 'RP11-23E10.4.0', 'RP11-556N21.1.0', 'IGHV1OR21-1.390530', 'RP11-206L10.10.0', 'RP11-35J10.5.0', 'MIR508.574513', 'LOC100132077.100132077', 'CTD-2532D12.4.0', 'TRBV20-1.28567', 'NPIPB6.728741', 'COX10-AS1.100874058', 'KRT17P4.339186', 'TRAV13-1.28671', 'TRBV6-9.28598', 'RP1-30E17.2.0', 'IGKV2D-29.28882', 'TRBV28.28559', 'TBC1D3P1-DHX40P1.653645', 'MIR526B.574468', 'TRBV5-7.28608', 'LOC101928823.101928823', 'LINC00511.400619', 'KRTAP10-4.386672', 'RP11-275O4.3.0', 'CPHL1P.389160', 'LOC105375875.105375875', 'RP11-260M19.2.0', 'TRAV19.28664', 'HIST2H3PS2.440686', 'LINC00857.439990', 'TRBV27.28560', 'LINC01331.104310351', 'MRPL42P4.346470', 'RP11-420N3.2.0', 'IGLV9-49.28773', 'CTD-2503O16.4.0', 'SPDYE18.100505767', 'LOC643542.643542', 'RPL39P5.553117', 'CHORDC2P.317775', 'RP11-3P22.2.0', 'CCRN4L.25819', 'IGHV1OR16-4.28312', 'TRBV7-7.28591', 'RP11-649A16.1.0', 'AL133247.2.0', 'LOC100287934.100287934', 'RP11-1060J15.4.0', 'HMGB3P5.645360', 'TUBBP1.92755', 'IGKV1-16.28938'
LGG_object@expression_table[1:5, 1:5]## A1BG.AS1.503538 A1BG.1 A1CF.29974 A2M.AS1.144571 A2M.2
## TCGA-CS-4938-01B 2.7407 2.4365 0 0.4432 8.9506
## TCGA-CS-4941-01A 1.6222 2.3834 0 1.7243 9.4713
## TCGA-CS-4942-01A 2.0342 2.4167 0 0.3698 9.3009
## TCGA-CS-4943-01A 1.5353 1.4604 0 0.3816 8.7217
## TCGA-CS-4944-01A 0.9567 1.0011 0 0.4874 8.2942
LGG_object@mutation_table[1:5, ]## Sample Gene Mutation Type
## 1 TCGA-CS-4938-01B PRPF8.10594 p.R1141C Missense_Mutation
## 2 TCGA-CS-4938-01B TPO.7173 p.G712S Missense_Mutation
## 3 TCGA-CS-4938-01B RPS19BP1.91582 p.K115E Missense_Mutation
## 4 TCGA-CS-4938-01B FGF5.2250 p.R205G Missense_Mutation
## 5 TCGA-CS-4938-01B KDM7A.80853 p.S318R Missense_Mutation
The LGG_object is passed to compute_complexes, which uses TDAmapper
and RayleighSelection R packages to create nerve complexes across a grid
of Mapper parameters (2D intervals and their percent overlap). We create
several nerve complexes across a broad range of parameters to ensure
stable results.
The LGG_object is populated with the topological representations and
the parameters used to make
them.
LGG_object <- compute_complexes(LGG_object, filter_method = 'KNN', k = 30, min_interval = 10, max_interval = 60, interval_step = 10, min_percent_overlap = 60, max_percent_overlap = 85, percent_step = 5)To check the validity of the options chosen in the pipeline so far, we want to visualize our data on the topological representations. We expect to see localization of mutated genes which have been previously identified as distinct markers of low grade glioma subtypes.
- IDH1 mutations in a subtype of astrocytoma
- ATRX mutations in a astrocytic gliomas
- CIC mutations in oligodendromas
We’ve chosen the topological representation created with 2D intervals =
30 and percent overlap = 75. More can be specified in a vector of
interval and percent pairs passed to which_complexes. By default, 3
representations with parameters in the middle of the parameter range are
chosen.
LGG_genes <- c('EGFR.1956', 'TP53.7157', 'IDH2.3418', 'CIC.23152')
plot_mapper(LGG_object, type = 'mutation', features = LGG_genes, which_complexes = c(30,75))## Plotting nerve complex with 2D intervals = 30 and percent overlap = 75
Images to be added soon
Filtering genes by mutation frequency, highest fraction of nonsynonymous mutations, and weak correlations between expression and mutation data
Genes can be filtered by
- Mutational frequency among all samples
- Those with the greatest ratio of nonsynonymous mutations to total mutations
- Associations between expression and mutation rates of a gene
For example, anticorrelations between expression and mutation rates can arise due to transcription-coupled DNA repair. To correct for this, we assess the similarity of expression and mutation profiles within the topological representations using Spearman's rank correlation coefficient.
Genes with a median q value in between the thresholds specified by the
upper_correlations_threshold and lower_correlations_threshold arguments
are not considered, as they do not display a strong correlation or
anticorrelation between expression and mutation rates.
LGG_object <- filter_genes(LGG_object, freq_threshold = 0.015, top_nonsyn_fraction = 350, upper_correlations_threshold = 0.9, lower_correlations_threshold = 1e-4)## Not considering the following genes with no expression data: 'ANKRD36C.400986', 'FRG1B.284802', 'GPR112.139378', 'GPR98.84059', 'HLA-A.3105', 'HLA-DQB2.3120', 'KRTAP1-5.83895', 'KRTAP4-11.653240', 'KRTAP4-8.728224', 'KRTAP4-9.100132386', 'NPIPA5.100288332', 'UBBP4.23666'
## Not considering the following 93 genes not displaying strong correlations/anticorrelations between mutation and expression data: 'ABCA7.10347', 'ACAN.176', 'ADAM28.10863', 'ADAMTS9.56999', 'AHNAK.79026', 'ARID1A.8289', 'ASPM.259266', 'BOD1L1.259282', 'CACNA1E.777', 'CD163L1.283316', 'CD209.30835', 'CELSR3.1951', 'CHD9.80205', 'CLIP1.6249', 'COL7A1.1294', 'CPAMD8.27151', 'CSF2RA.1438', 'CSMD3.114788', 'DCAF12L2.340578', 'DCP1B.196513', 'DMBT1.1755', 'DMD.1756', 'DNAH17.8632', 'DNAH7.56171', 'DNAH8.1769', 'DNMT3A.1788', 'DOCK5.80005', 'DRC7.84229', 'F5.2153', 'F8.2157', 'FAT4.79633', 'FBN2.2201', 'FLG.2312', 'FRAS1.80144', 'FSTL5.56884', 'HECTD4.283450', 'HIVEP3.59269', 'HRNR.388697', 'HTR3A.3359', 'IDH1.3417', 'IDH2.3418', 'IGF1R.3480', 'IL32.9235', 'KCNN2.3781', 'KIF16B.55614', 'KIF2B.84643', 'KMT2A.4297', 'LAMA3.3909', 'LRP1.4035', 'LRP1B.53353', 'LRP2.4036', 'LRRK1.79705', 'MAML3.55534', 'MUC5B.727897', 'MYH1.4619', 'MYH11.4629', 'MYH13.8735', 'MYH4.4622', 'MYO15A.51168', 'NBPF1.55672', 'NBPF10.100132406', 'NEB.4703', 'OGT.8473', 'PCDH19.57526', 'PCDHA2.56146', 'PCDHB3.56132', 'PCLO.27445', 'PDGFRA.5156', 'PHF3.23469', 'PKHD1.5314', 'PLEC.5339', 'PLXNA1.5361', 'POTEC.388468', 'PRDM9.56979', 'PTPRZ1.5803', 'RANBP2.5903', 'RELN.5649', 'RGAG1.57529', 'RIPK4.54101', 'ROBO3.64221', 'ROS1.6098', 'RYR1.6261', 'RYR2.6262', 'SETD2.29072', 'SPATA31E1.286234', 'TENM1.10178', 'TMEM132B.114795', 'TNXB.7148', 'TRRAP.8295', 'TTN.7273', 'VPS13B.157680', 'WDFY3.23001', 'ZNF638.27332'
Filtered genes are assessed for localization across the topological
representations using RayleighSelection. Localization is quantified
via a p value, estimated by a similar permutation scheme as noted above.
The false discovery rate is controlled using the Benjamini-Hochberg
procedure, which results in an accompanying localization q value.
Note: compute_gene_localization is the most time-intensive function
of TDAmut and can take a couple hours. Consider using the num_cores
argument to parallelize this function.
LGG_object <- compute_gene_localization(LGG_object, num_permutations = 5000, num_cores = 1)Results are summarized and stored in the summary_matrix slot of the
TDAmut_object. Genes with a median localization q value below a
user-defined threshold should be considered significant. These genes
are predicted to be associated with global expression patterns over a
subset of tumors.
LGG_object@summary_matrix[1:8,]## combined.p0 q0 expression_first_quartile expression_median expression_third_quartile cor_median_p cor_median_q cor_median_rho nonsyn_count
## ATRX.546 0.000000e+00 0.0000000000 3.060450 3.72140 4.425275 2.146322e-76 5.172635e-74 -0.7005306 204
## CIC.23152 0.000000e+00 0.0000000000 4.821300 5.16165 5.496125 4.439870e-61 5.350044e-59 -0.6486133 113
## EGFR.1956 0.000000e+00 0.0000000000 4.331775 5.32795 6.205900 1.000000e+00 1.000000e+00 0.3216203 36
## FUBP1.8880 0.000000e+00 0.0000000000 4.586700 5.03025 5.417500 9.635606e-30 7.641520e-28 -0.4790635 48
## NF1.4763 0.000000e+00 0.0000000000 4.817325 5.15865 5.509025 3.979206e-16 1.917977e-14 -0.3743460 34
## PTEN.5728 0.000000e+00 0.0000000000 4.211950 4.49610 4.748700 2.804993e-23 1.690008e-21 -0.4442587 24
## TP53.7157 0.000000e+00 0.0000000000 5.190550 5.65895 6.052850 7.916889e-10 3.193411e-08 -0.2878403 261
## NOTCH1.4851 2.785176e-05 0.0005152575 5.065250 5.64145 6.078500 9.999999e-01 1.000000e+00 0.2156026 44