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pmid:36844983
Bioinformatics Analysis of Next Generation Sequencing Data Identifies Molecular Biomarkers Associated With Type 2 Diabetes Mellitus.
Varun Alur · Varshita Raju · Basavaraj Vastrad · Chanabasayya Vastrad · Satish Kavatagimath · Shivakumar Kotturshetti
Clinical medicine insights. Endocrinology and diabetes · 2023 doi:10.1177/11795514231155635
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Experiment
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Data
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Analysis
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Complete file
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The aim of the present investigation was to identify gene signature specific to T2DM.\nMethods: The next generation sequencing (NGS) dataset GSE81608 was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA (micro RNA)-hub gene regulatory network construction and TF (transcription factor)-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the prognostic value of hub genes.\nResults: A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins, and metabolism. The top centrality hub genes APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1 were screened out as the critical genes. ROC analysis provides prognostic value of hub genes.\nConclusion: The potential crucial genes, especially APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1, might be linked with risk of T2DM. Our study provided novel insights of T2DM into genetics, molecular pathogenesis, and novel therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Limma package in R software was used to search for in messenger RNAs (mRNAs; DEGs) that were differentially expressed between T2DM and healthy control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36844983", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "Limma package in R software was used to search for in messenger RNAs (mRNAs; DEGs) that were differentially expressed between T2DM and healthy control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of data and materials: The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/) repository [(GSE81608) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81608)].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36844983", "locator": "sections[22] \"Declarations\" paragraph 1", "quote": "Availability of data and materials: The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/) repository [(GSE81608) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81608)]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 927 genes were identified to be differentially expressed between T2DM and normal control samples with the threshold of adjusted P-value of <.05, and logFC value were >0.181 for up regulated genes and <−0.27 for down regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36844983", "locator": "sections[11] \"Identification of DEGs\" paragraph 2", "quote": "A total of 927 genes were identified to be differentially expressed between T2DM and normal control samples with the threshold of adjusted P-value of <.05, and logFC value were >0.181 for up regulated genes and <−0.27 for down regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 927 genes were identified to be differentially expressed between T2DM and normal control samples with the threshold of adjusted P-value of <.05, and logFC value were >0.181 for up regulated genes and <−0.27 for down regulated genes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36844983"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE81608"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE81608"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36844983", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/11795514231155635", "sha256": 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"GSM2158496", "GSM2158497", "GSM2158498", "GSM2158499", "GSM2158500", "GSM2158501", "GSM2158502", "GSM2158503", "GSM2158504", "GSM2158505", "GSM2158506", "GSM2158507", "GSM2158508", "GSM2158509", "GSM2158510", "GSM2158511", "GSM2158512", "GSM2158513", "GSM2158514", "GSM2158515", "GSM2158516", "GSM2158517", "GSM2158518", "GSM2158519", "GSM2158520", "GSM2158521", "GSM2158522", "GSM2158523", "GSM2158524", "GSM2158525", "GSM2158526", "GSM2158527", "GSM2158528", "GSM2158529", "GSM2158530", "GSM2158531", "GSM2158532", "GSM2158533", "GSM2158534", "GSM2158535", "GSM2158536", "GSM2158537", "GSM2158538", "GSM2158539", "GSM2158540", "GSM2158541", "GSM2158542", "GSM2158543", "GSM2158544", "GSM2158545", "GSM2158546", "GSM2158547", "GSM2158548", "GSM2158549", "GSM2158550", "GSM2158551", "GSM2158552", "GSM2158553", "GSM2158554", "GSM2158555", "GSM2158556", "GSM2158557", "GSM2158558", "GSM2158559", "GSM2158560", "GSM2158561", "GSM2158562", "GSM2158563", "GSM2158564", "GSM2158565", "GSM2158566", "GSM2158567", "GSM2158568", "GSM2158569", "GSM2158570", "GSM2158571", "GSM2158572", "GSM2158573", "GSM2158574", "GSM2158575", "GSM2158576", "GSM2158577", "GSM2158578", "GSM2158579", "GSM2158580", "GSM2158581", "GSM2158582", "GSM2158583", "GSM2158584", "GSM2158585", "GSM2158586", "GSM2158587", "GSM2158588", "GSM2158589", "GSM2158590", "GSM2158591", "GSM2158592", "GSM2158593", "GSM2158594", "GSM2158595", "GSM2158596", "GSM2158597", "GSM2158598", "GSM2158599", "GSM2158600", "GSM2158601", "GSM2158602", "GSM2158603", "GSM2158604", "GSM2158605", "GSM2158606", "GSM2158607", "GSM2158608", "GSM2158609", "GSM2158610", "GSM2158611", "GSM2158612", "GSM2158613", "GSM2158614", "GSM2158615", "GSM2158616", "GSM2158617", "GSM2158618", "GSM2158619", "GSM2158620", "GSM2158621", "GSM2158622", "GSM2158623", "GSM2158624", "GSM2158625", "GSM2158626", "GSM2158627", "GSM2158628", "GSM2158629", "GSM2158630", "GSM2158631", "GSM2158632", "GSM2158633", "GSM2158634", "GSM2158635", "GSM2158636", "GSM2158637", "GSM2158638", "GSM2158639", "GSM2158640", "GSM2158641", "GSM2158642", "GSM2158643", "GSM2158644", "GSM2158645", "GSM2158646", "GSM2158647", "GSM2158648", "GSM2158649", "GSM2158650", "GSM2158651", "GSM2158652", "GSM2158653", "GSM2158654", "GSM2158655", "GSM2158656", "GSM2158657", "GSM2158658", "GSM2158659", "GSM2158660", "GSM2158661", "GSM2158662", "GSM2158663", "GSM2158664", "GSM2158665", "GSM2158666", "GSM2158667", "GSM2158668", "GSM2158669", "GSM2158670", "GSM2158671", "GSM2158672", "GSM2158673", "GSM2158674", "GSM2158675", "GSM2158676", "GSM2158677", "GSM2158678", "GSM2158679", "GSM2158680", "GSM2158681", "GSM2158682", "GSM2158683", "GSM2158684", "GSM2158685", "GSM2158686", "GSM2158687", "GSM2158688", "GSM2158689", "GSM2158690", "GSM2158691", "GSM2158692", "GSM2158693", "GSM2158694", "GSM2158695", "GSM2158696", "GSM2158697", "GSM2158698", "GSM2158699", "GSM2158700", "GSM2158701", "GSM2158702", "GSM2158703", "GSM2158704", "GSM2158705", "GSM2158706", "GSM2158707", "GSM2158708", "GSM2158709", "GSM2158710", "GSM2158711", "GSM2158712", "GSM2158713", "GSM2158714", "GSM2158715", "GSM2158716", "GSM2158717", "GSM2158718", "GSM2158719", "GSM2158720", "GSM2158721", "GSM2158722", "GSM2158723", "GSM2158724", "GSM2158725", "GSM2158726", "GSM2158727", "GSM2158728", "GSM2158729", "GSM2158730", "GSM2158731", "GSM2158732", "GSM2158733", "GSM2158734", "GSM2158735", "GSM2158736", "GSM2158737", "GSM2158738", "GSM2158739", "GSM2158740", "GSM2158741", "GSM2158742", "GSM2158743", "GSM2158744", "GSM2158745", "GSM2158746", "GSM2158747", "GSM2158748", "GSM2158749", "GSM2158750", "GSM2158751", "GSM2158752", "GSM2158753", "GSM2158754", "GSM2158755", "GSM2158756", "GSM2158757", "GSM2158758", "GSM2158759", "GSM2158760", "GSM2158761", "GSM2158762", "GSM2158763", "GSM2158764", "GSM2158765", "GSM2158766", "GSM2158767", "GSM2158768", "GSM2158769", "GSM2158770", "GSM2158771", "GSM2158772", "GSM2158773", "GSM2158774", "GSM2158775", "GSM2158776", "GSM2158777", "GSM2158778", "GSM2158779", "GSM2158780", "GSM2158781", "GSM2158782", "GSM2158783", "GSM2158784", "GSM2158785", "GSM2158786", "GSM2158787", "GSM2158788", "GSM2158789", "GSM2158790", "GSM2158791", "GSM2158792", "GSM2158793", "GSM2158794", "GSM2158795", "GSM2158796", "GSM2158797", "GSM2158798", "GSM2158799", "GSM2158800", "GSM2158801", "GSM2158802", "GSM2158803", "GSM2158804", "GSM2158805", "GSM2158806", "GSM2158807", "GSM2158808", "GSM2158809", "GSM2158810", "GSM2158811", "GSM2158812", "GSM2158813", "GSM2158814", "GSM2158815", "GSM2158816", "GSM2158817", "GSM2158818", "GSM2158819", "GSM2158820", "GSM2158821", "GSM2158822", "GSM2158823", "GSM2158824", "GSM2158825", "GSM2158826", "GSM2158827", "GSM2158828", "GSM2158829", "GSM2158830", "GSM2158831", "GSM2158832", "GSM2158833", "GSM2158834", "GSM2158835", "GSM2158836", "GSM2158837", "GSM2158838", "GSM2158839", "GSM2158840", "GSM2158842", "GSM2158843", "GSM2158844", "GSM2158846", "GSM2158848", "GSM2158849", "GSM2158850", "GSM2158852", "GSM2158853", "GSM2158855", "GSM2158856", "GSM2158858", "GSM2158859", "GSM2158861", "GSM2158862", "GSM2158863", "GSM2158865", "GSM2158866", "GSM2158868", "GSM2158869", "GSM2158871", "GSM2158872", "GSM2158874", "GSM2158875", "GSM2158877", "GSM2158878", "GSM2158879", "GSM2158881", "GSM2158882", "GSM2158884", "GSM2158885", "GSM2158887", "GSM2158888", "GSM2158889", "GSM2158891", "GSM2158892", "GSM2158894", "GSM2158895", "GSM2158896", "GSM2158898", "GSM2158899", "GSM2158901", "GSM2158902", "GSM2158904", "GSM2158906", "GSM2158907", "GSM2158908", "GSM2158910", "GSM2158911", "GSM2158913", "GSM2158914", "GSM2158916", "GSM2158917", "GSM2158919", "GSM2158920", "GSM2158922", "GSM2158923", "GSM2158925", "GSM2158926", "GSM2158928", "GSM2158929", "GSM2158931", "GSM2158932", "GSM2158934", "GSM2158935", "GSM2158936", "GSM2158937", "GSM2158938", "GSM2158939", "GSM2158940", "GSM2158941", "GSM2158942", "GSM2158943", "GSM2158944", "GSM2158945", "GSM2158946", "GSM2158947", "GSM2158948", "GSM2158949", "GSM2158950", "GSM2158951", "GSM2158952", "GSM2158953", "GSM2158954", "GSM2158955", "GSM2158956", "GSM2158957", "GSM2158958", "GSM2158959", "GSM2158960", "GSM2158961", "GSM2158962", "GSM2158963", "GSM2158964", "GSM2158965", "GSM2158966", "GSM2158967", "GSM2158968", "GSM2158969", "GSM2158970", "GSM2158971", "GSM2158972", "GSM2158973", "GSM2158974", "GSM2158975", "GSM2158976", "GSM2158977", "GSM2158978", "GSM2158979", "GSM2158980", "GSM2158981", "GSM2158982", "GSM2158983", "GSM2158984", "GSM2158985", "GSM2158986", "GSM2158987", "GSM2158988", "GSM2158989", "GSM2158990", "GSM2158991", "GSM2158992", "GSM2158993", "GSM2158994", "GSM2158995", "GSM2158996", "GSM2158997", "GSM2158998", "GSM2158999", "GSM2159000", "GSM2159001", "GSM2159002", "GSM2159003", "GSM2159004", "GSM2159005", "GSM2159006", "GSM2159007", "GSM2159008", "GSM2159009", "GSM2159010", "GSM2159011", "GSM2159012", "GSM2159013", "GSM2159014", "GSM2159015", "GSM2159016", "GSM2159017", "GSM2159018", "GSM2159019", "GSM2159020", "GSM2159021", "GSM2159022", "GSM2159023", "GSM2159024", "GSM2159025", "GSM2159026", "GSM2159027", "GSM2159028", "GSM2159029", "GSM2159030", "GSM2159031", "GSM2159032", "GSM2159033", "GSM2159034", "GSM2159035", "GSM2159036", "GSM2159037", "GSM2159038", "GSM2159039", "GSM2159040", "GSM2159041", "GSM2159042", "GSM2159043", "GSM2159044", "GSM2159045", "GSM2159046", "GSM2159047", "GSM2159048", "GSM2159049", "GSM2159050", "GSM2159051", "GSM2159052", "GSM2159053", "GSM2159054", "GSM2159055", "GSM2159056", "GSM2159057", "GSM2159058", "GSM2159059", "GSM2159060", "GSM2159061", "GSM2159062", "GSM2159063", "GSM2159064", "GSM2159065", "GSM2159066", "GSM2159067", "GSM2159068", "GSM2159069", "GSM2159070", "GSM2159071", "GSM2159072", "GSM2159073", "GSM2159074", "GSM2159075", "GSM2159076", "GSM2159077", "GSM2159078", "GSM2159079", "GSM2159080", "GSM2159081", "GSM2159082", "GSM2159083", "GSM2159084", "GSM2159085", "GSM2159086", "GSM2159087", "GSM2159088", "GSM2159089", "GSM2159090", "GSM2159091", "GSM2159092", "GSM2159093", "GSM2159094", "GSM2159095", "GSM2159096", "GSM2159097", "GSM2159098", "GSM2159099", "GSM2159100", "GSM2159101", "GSM2159102", "GSM2159103", "GSM2159104", "GSM2159105", "GSM2159106", "GSM2159107", "GSM2159108", "GSM2159109", "GSM2159110", "GSM2159111", "GSM2159112", "GSM2159113", "GSM2159114", "GSM2159115", "GSM2159116", "GSM2159117", "GSM2159118", "GSM2159119", "GSM2159120", "GSM2159121", "GSM2159122", "GSM2159123", "GSM2159124", "GSM2159125", "GSM2159126", "GSM2159127", "GSM2159128", "GSM2159129", "GSM2159130", "GSM2159131", "GSM2159132", "GSM2159133", "GSM2159134", "GSM2159135", "GSM2159136", "GSM2159137", "GSM2159138", "GSM2159139", "GSM2159140", "GSM2159141", "GSM2159142", "GSM2159143", "GSM2159144", "GSM2159145", "GSM2159146", "GSM2159147", "GSM2159148", "GSM2159149", "GSM2159150", "GSM2159151", "GSM2159152", "GSM2159153", "GSM2159154", "GSM2159155", "GSM2159156", "GSM2159157", "GSM2159158", "GSM2159159", "GSM2159160", "GSM2159161", "GSM2159162", "GSM2159163", "GSM2159164", "GSM2159165", "GSM2159166", "GSM2159167", "GSM2159168", "GSM2159169", "GSM2159170", "GSM2159171", "GSM2159172", "GSM2159173", "GSM2159174", "GSM2159175", "GSM2159176", "GSM2159177", "GSM2159178", "GSM2159179", "GSM2159180", "GSM2159181", "GSM2159182", "GSM2159183", "GSM2159184", "GSM2159185", "GSM2159186", "GSM2159187", "GSM2159188", "GSM2159189", "GSM2159190", "GSM2159191", "GSM2159192", "GSM2159193", "GSM2159194", "GSM2159195", "GSM2159196", "GSM2159197", "GSM2159198", "GSM2159199", "GSM2159200", "GSM2159201", "GSM2159202", "GSM2159203", "GSM2159204", "GSM2159205", "GSM2159206", "GSM2159207", "GSM2159208", "GSM2159209", "GSM2159210", "GSM2159211", "GSM2159212", "GSM2159213", "GSM2159214", "GSM2159215", "GSM2159216", "GSM2159217", "GSM2159218", "GSM2159219", "GSM2159220", "GSM2159221", "GSM2159222", "GSM2159223", "GSM2159224", "GSM2159225", "GSM2159226", "GSM2159227", "GSM2159228", "GSM2159229", "GSM2159230", "GSM2159231", "GSM2159235", "GSM2159238", "GSM2159240", "GSM2159243", "GSM2159245", "GSM2159248", "GSM2159251", "GSM2159254", "GSM2159256", "GSM2159258", "GSM2159261", "GSM2159263", "GSM2159266", "GSM2159269", "GSM2159271", "GSM2159274", "GSM2159277", "GSM2159279", "GSM2159280", "GSM2159281", "GSM2159282", "GSM2159283", "GSM2159284", "GSM2159285", "GSM2159286", "GSM2159287", "GSM2159288", "GSM2159289", "GSM2159290", "GSM2159291", "GSM2159292", "GSM2159293", "GSM2159294", "GSM2159295", "GSM2159296", "GSM2159297", "GSM2159298", "GSM2159299", "GSM2159300", "GSM2159301", "GSM2159302", "GSM2159303", "GSM2159304", "GSM2159305", "GSM2159306", "GSM2159307", "GSM2159308", "GSM2159309", "GSM2159310", "GSM2159311", "GSM2159312", "GSM2159313", "GSM2159314", "GSM2159315", "GSM2159316", "GSM2159317", "GSM2159318", "GSM2159319", "GSM2159320", "GSM2159321", "GSM2159322", "GSM2159323", "GSM2159324", "GSM2159325", "GSM2159326", "GSM2159327", "GSM2159328", "GSM2159329", "GSM2159330", "GSM2159331", "GSM2159332", "GSM2159333", "GSM2159334", "GSM2159335", "GSM2159336", "GSM2159337", "GSM2159338", "GSM2159339", "GSM2159340", "GSM2159341", "GSM2159342", "GSM2159343", "GSM2159344", "GSM2159345", "GSM2159346", "GSM2159347", "GSM2159348", "GSM2159349", "GSM2159350", "GSM2159351", "GSM2159352", "GSM2159353", "GSM2159354", "GSM2159355", "GSM2159356", "GSM2159357", "GSM2159358", "GSM2159359", "GSM2159360", "GSM2159361", "GSM2159362", "GSM2159363", "GSM2159364", "GSM2159365", "GSM2159366", "GSM2159367", "GSM2159368", "GSM2159369", "GSM2159370", "GSM2159371", "GSM2159372", "GSM2159373", "GSM2159374", "GSM2159375", "GSM2159376", "GSM2159377", "GSM2159378", "GSM2159379", "GSM2159380", "GSM2159381", "GSM2159382", "GSM2159383", "GSM2159384", "GSM2159385", "GSM2159386", "GSM2159387", "GSM2159388", "GSM2159389", "GSM2159390", "GSM2159391", "GSM2159392", "GSM2159393", "GSM2159394", "GSM2159395", "GSM2159396", "GSM2159397", "GSM2159398", "GSM2159399", "GSM2159400", "GSM2159401", "GSM2159402", "GSM2159403", "GSM2159404", "GSM2159405", "GSM2159406", "GSM2159407", "GSM2159408", "GSM2159409", "GSM2159410", "GSM2159411", "GSM2159412", "GSM2159413", "GSM2159414", "GSM2159415", "GSM2159416", "GSM2159417", "GSM2159418", "GSM2159419", "GSM2159420", "GSM2159421", "GSM2159422", "GSM2159423", "GSM2159424", "GSM2159425", "GSM2159426", "GSM2159427", "GSM2159428", "GSM2159429", "GSM2159430", "GSM2159431", "GSM2159432", "GSM2159433", "GSM2159434", "GSM2159435", "GSM2159436", "GSM2159437", "GSM2159438", "GSM2159439", "GSM2159440", "GSM2159441", "GSM2159442", "GSM2159443", "GSM2159444", "GSM2159445", "GSM2159446", "GSM2159447", "GSM2159448", "GSM2159449", "GSM2159450", "GSM2159451", "GSM2159452", "GSM2159453", "GSM2159454", "GSM2159455", "GSM2159456", "GSM2159457", "GSM2159458", "GSM2159459", "GSM2159460", "GSM2159461", "GSM2159462", "GSM2159463", "GSM2159464", "GSM2159465", "GSM2159466", "GSM2159467", "GSM2159468", "GSM2159469", "GSM2159470", "GSM2159471", "GSM2159472", "GSM2159473", "GSM2159474", "GSM2159475", "GSM2159476", "GSM2159477", "GSM2159478", "GSM2159479", "GSM2159480", "GSM2159481", "GSM2159482", "GSM2159483", "GSM2159484", "GSM2159485", "GSM2159486", "GSM2159487", "GSM2159488", "GSM2159489", "GSM2159490", "GSM2159491", "GSM2159492", "GSM2159493", "GSM2159494", "GSM2159495", "GSM2159496", "GSM2159497", "GSM2159498", "GSM2159499", "GSM2159500", "GSM2159501", "GSM2159502", "GSM2159503", "GSM2159504", "GSM2159505", "GSM2159506", "GSM2159507", "GSM2159508", "GSM2159509", "GSM2159510", "GSM2159511", "GSM2159512", "GSM2159513", "GSM2159514", "GSM2159515", "GSM2159516", "GSM2159517", "GSM2159518", "GSM2159519", "GSM2159520", "GSM2159521", "GSM2159522", "GSM2159523", "GSM2159524", "GSM2159525", "GSM2159526", "GSM2159527", "GSM2159528", "GSM2159529", "GSM2159530", "GSM2159531", "GSM2159532", "GSM2159533", "GSM2159534", "GSM2159535", "GSM2159536", "GSM2159537", "GSM2159538", "GSM2159539", "GSM2159540", "GSM2159541", "GSM2159542", "GSM2159543", "GSM2159544", "GSM2159545", "GSM2159546", "GSM2159547", "GSM2159548", "GSM2159549", 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