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pmid:39033204
Angiogenesis related genes based prognostic model of glioma patients developed by multi-omics approach.
Zhimin Liu · Hongjun Fan · XuKai Liu · Chao Liu
Discover oncology · 2024 doi:10.1007/s12672-024-01126-6
Paper
complete
Experiment
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Data
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Analysis
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Execution
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Complete file
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Angiogenesis, the formation of new blood vessels, is a tightly regulated process involving endothelial cell activation, proliferation, and migration. In cancer, angiogenesis becomes dysregulated, leading to excessive blood vessel formation.\nMETHODS: We enrolled bulk data of TCGA-LGG/GBM, CGGA-693, and CGGA-325 cohorts, scRNA data of GSE162631, GSE84465, and GSE138794 cohorts. Identification of malignant cells was conducted by \"copycat\" R package. The \"AUCell\" R package scored the activity of target gene set of each single cell. Consensus clustering was applied using the \"ConsensusClusterPlus\" R package, while tumor-infiltrating immune cells were determined using \"IOBR\" R package. To construct a prognostic model, we used LASSO and multiCOX algorithms based on the expression levels of the 15 hub genes, the efficacy of which was verified by KM and ROC analysis.\nRESULTS: We identified 4 different malignant cell subclusters in glioma and disclosed their distinct gene expression patterns and interactions within TME. We identified differentially expressed immune-related genes (DE-ARGs) in glioma and found 15 genes that were specifically expressed in the malignant glioma cell populations. Glioma cells with higher expression of these DE-ARGs were associated with gliogenesis, glial cell development, and vasculature development. We found that tumor-infiltrating monocytes were the main interacting cell type within glioma TME. Using the expression patterns of the 15 screened DE-ARGs, we categorized glioma samples into 2 molecular clusters with distinct immune features, suggesting a possible relationship between angiogenesis and immune activation and recruitment. We constructed a prognostic model based on the expression levels of the 15 DE-ARGs and evaluated its predictive ability for glioma patient outcomes, which displayed exceedingly high efficacy.\nCONCLUSION: We characterized different malignant cell subclusters in glioma and investigate their gene expression patterns and interactions within TME. We constructed a prognostic model based on the expression levels of the 15 DE-ARGs and evaluated its predictive ability for glioma patient outcomes, which displayed exceedingly high efficacy.", "claims": [{"id": "claim-method", "statement": "Based on 15 hub genes, a prognostic model was constructed using LASSO and multiCOX.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39033204", "locator": "sections[9] \"Prognosis model construction and nomogram model establishment\" paragraph 2", "quote": "Based on 15 hub genes, a prognostic model was constructed using LASSO and multiCOX."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data could be obtained from TCGA database,or coresponding author after the requestion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39033204", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The data could be obtained from TCGA database,or coresponding author after the requestion."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A LASSO and multiCOX prognostic model based on 15 DE-ARGs identified inferior outcomes for patients with higher risk scores across all three cohorts and achieved AUC values above 0.9 at 1 and 3 years postoperatively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39033204", "locator": "sections[17] \"Prognostic model construction and nomogram establishment\" paragraph 2", "quote": "We found that a unanimous inferior clinical outcome of glioma patients of relatively higher risk value across all 3 cohorts, which were further support by an exceedingly satisfactory AUC value above 0.9 at 1 year and 3 years post-operative time points (Fig. 9c)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A LASSO and multiCOX prognostic model based on 15 DE-ARGs identified inferior outcomes for patients with higher risk scores across all three cohorts and achieved AUC values above 0.9 at 1 and 3 years postoperatively.", "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:39033204"], "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. 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"GSM2245226", "GSM2245227", "GSM2245228", "GSM2245229", "GSM2245230", "GSM2245231", "GSM2245232", "GSM2245233", "GSM2245234", "GSM2245235", "GSM2245236", "GSM2245237", "GSM2245238", "GSM2245239", "GSM2245240", "GSM2245241", "GSM2245242", "GSM2245243", "GSM2245244", "GSM2245245", "GSM2245246", "GSM2245247", "GSM2245248", "GSM2245249", "GSM2245250", "GSM2245251", "GSM2245252", "GSM2245253", "GSM2245254", "GSM2245255", "GSM2245256", "GSM2245257", "GSM2245258", "GSM2245259", "GSM2245260", "GSM2245261", "GSM2245262", "GSM2245263", "GSM2245264", "GSM2245265", "GSM2245266", "GSM2245267", "GSM2245268", "GSM2245269", "GSM2245270", "GSM2245271", "GSM2245272", "GSM2245273", "GSM2245274", "GSM2245275", "GSM2245276", "GSM2245277", "GSM2245278", "GSM2245279", "GSM2245280", "GSM2245281", "GSM2245282", "GSM2245283", "GSM2245284", "GSM2245285", "GSM2245286", "GSM2245287", "GSM2245288", "GSM2245289", "GSM2245290", "GSM2245291", "GSM2245292", "GSM2245293", "GSM2245294", "GSM2245295", "GSM2245296", "GSM2245297", "GSM2245298", "GSM2245299", "GSM2245300", "GSM2245301", "GSM2245302", "GSM2245303", "GSM2245304", "GSM2245305", "GSM2245306", "GSM2245307", "GSM2245308", "GSM2245309", "GSM2245310", "GSM2245311", "GSM2245312", "GSM2245313", "GSM2245314", "GSM2245315", "GSM2245316", "GSM2245317", "GSM2245318", "GSM2245319", "GSM2245320", "GSM2245321", "GSM2245322", "GSM2245323", "GSM2245324", "GSM2245325", "GSM2245326", "GSM2245327", "GSM2245328", "GSM2245329", "GSM2245330", "GSM2245331", "GSM2245332", "GSM2245333", "GSM2245334", "GSM2245335", "GSM2245336", "GSM2245337", "GSM2245338", "GSM2245339", "GSM2245340", "GSM2245341", "GSM2245342", "GSM2245343", "GSM2245344", "GSM2245345", "GSM2245346", "GSM2245347", "GSM2245348", "GSM2245349", "GSM2245350", "GSM2245351", "GSM2245352", "GSM2245353", "GSM2245354", "GSM2245355", "GSM2245356", "GSM2245357", "GSM2245358", "GSM2245359", "GSM2245360", "GSM2245361", "GSM2245362", "GSM2245363", "GSM2245364", "GSM2245365", "GSM2245366", "GSM2245367", "GSM2245368", "GSM2245369", "GSM2245370", "GSM2245371", "GSM2245372", "GSM2245373", "GSM2245374", "GSM2245375", "GSM2245376", "GSM2245377", "GSM2245378", "GSM2245379", "GSM2245380", "GSM2245381", "GSM2245382", "GSM2245383", "GSM2245384", "GSM2245385", "GSM2245386", "GSM2245387", "GSM2245388", "GSM2245389", "GSM2245390", "GSM2245391", "GSM2245392", "GSM2245393", "GSM2245394", "GSM2245395", "GSM2245396", "GSM2245397", "GSM2245398", "GSM2245399", "GSM2245400", "GSM2245401", "GSM2245402", "GSM2245403", "GSM2245404", "GSM2245405", "GSM2245406", "GSM2245407", "GSM2245408", "GSM2245409", "GSM2245410", "GSM2245411", "GSM2245412", "GSM2245413", "GSM2245414", "GSM2245415", "GSM2245416", "GSM2245417", "GSM2245418", "GSM2245419", "GSM2245420", "GSM2245421", "GSM2245422", "GSM2245423", "GSM2245424", "GSM2245425", "GSM2245426", "GSM2245427", "GSM2245428", "GSM2245429", "GSM2245430", "GSM2245431", "GSM2245432", "GSM2245433", "GSM2245434", "GSM2245435", "GSM2245436", "GSM2245437", "GSM2245438", "GSM2245439", "GSM2245440", "GSM2245441", "GSM2245442", "GSM2245443", "GSM2245444", "GSM2245445", "GSM2245446", "GSM2245447", "GSM2245448", "GSM2245449", "GSM2245450", "GSM2245451", "GSM2245452", "GSM2245453", "GSM2245454", "GSM2245455", "GSM2245456", "GSM2245457", "GSM2245458", "GSM2245459", "GSM2245460", "GSM2245461", "GSM2245462", "GSM2245463", "GSM2245464", "GSM2245465", "GSM2245466", "GSM2245467", "GSM2245468", "GSM2245469", "GSM2245470", "GSM2245471", "GSM2245472", "GSM2245473", "GSM2245474", "GSM2245475", "GSM2245476", "GSM2245477", "GSM2245478", "GSM2245479", "GSM2245480", "GSM2245481", "GSM2245482", "GSM2245483", "GSM2245484", "GSM2245485", "GSM2245486", "GSM2245487", "GSM2245488", "GSM2245489", "GSM2245490", "GSM2245491", "GSM2245492", "GSM2245493", "GSM2245494", "GSM2245495", "GSM2245496", "GSM2245497", "GSM2245498", "GSM2245499", "GSM2245500", "GSM2245501", "GSM2245502", "GSM2245503", "GSM2245504", "GSM2245505", "GSM2245506", "GSM2245507", "GSM2245508", "GSM2245509", "GSM2245510", "GSM2245511", "GSM2245512", "GSM2245513", "GSM2245514", "GSM2245515", "GSM2245516", "GSM2245517", "GSM2245518", "GSM2245519", "GSM2245520", "GSM2245521", "GSM2245522", "GSM2245523", "GSM2245524", "GSM2245525", "GSM2245526", "GSM2245527", "GSM2245528", "GSM2245529", "GSM2245530", "GSM2245531", "GSM2245532", "GSM2245533", "GSM2245534", "GSM2245535", "GSM2245536", "GSM2245537", "GSM2245538", "GSM2245539", "GSM2245540", "GSM2245541", "GSM2245542", "GSM2245543", "GSM2245544", "GSM2245545", "GSM2245546", "GSM2245547", "GSM2245548", "GSM2245549", "GSM2245550", "GSM2245551", "GSM2245552", "GSM2245553", "GSM2245554", "GSM2245555", "GSM2245556", "GSM2245557", "GSM2245558", "GSM2245559", "GSM2245560", "GSM2245561", "GSM2245562", "GSM2245563", "GSM2245564", "GSM2245565", "GSM2245566", "GSM2245567", "GSM2245568", "GSM2245569", "GSM2245570", "GSM2245571", "GSM2245572", "GSM2245573", "GSM2245574", "GSM2245575", "GSM2245576", "GSM2245577", "GSM2245578", "GSM2245579", "GSM2245580", "GSM2245581", "GSM2245582", "GSM2245583", "GSM2245584", "GSM2245585", "GSM2245586", "GSM2245587", "GSM2245588", "GSM2245589", "GSM2245590", "GSM2245591", "GSM2245592", "GSM2245593", "GSM2245594", "GSM2245595", "GSM2245596", "GSM2245597", "GSM2245598", "GSM2245599", "GSM2245600", "GSM2245601", "GSM2245602", "GSM2245603", "GSM2245604", "GSM2245605", "GSM2245606", "GSM2245607", "GSM2245608", "GSM2245609", "GSM2245610", "GSM2245611", "GSM2245612", "GSM2245613", "GSM2245614", "GSM2245615", "GSM2245616", "GSM2245617", "GSM2245618", "GSM2245619", "GSM2245620", "GSM2245621", "GSM2245622", "GSM2245623", "GSM2245624", "GSM2245625", "GSM2245626", "GSM2245627", "GSM2245628", "GSM2245629", "GSM2245630", "GSM2245631", "GSM2245632", "GSM2245633", "GSM2245634", "GSM2245635", "GSM2245636", "GSM2245637", "GSM2245638", "GSM2245639", "GSM2245640", "GSM2245641", "GSM2245642", "GSM2245643", "GSM2245644", "GSM2245645", "GSM2245646", "GSM2245647", "GSM2245648", "GSM2245649", "GSM2245650", "GSM2245651", "GSM2245652", "GSM2245653", "GSM2245654", "GSM2245655", "GSM2245656", "GSM2245657", "GSM2245658", "GSM2245659", "GSM2245660", "GSM2245661", "GSM2245662", "GSM2245663", "GSM2245664", "GSM2245665", "GSM2245666", "GSM2245667", "GSM2245668", "GSM2245669", "GSM2245670", "GSM2245671", "GSM2245672", "GSM2245673", "GSM2245674", "GSM2245675", "GSM2245676", "GSM2245677", "GSM2245678", "GSM2245679", "GSM2245680", "GSM2245681", "GSM2245682", "GSM2245683", "GSM2245684", "GSM2245685", "GSM2245686", "GSM2245687", "GSM2245688", "GSM2245689", "GSM2245690", "GSM2245691", "GSM2245692", "GSM2245693", "GSM2245694", "GSM2245695", "GSM2245696", "GSM2245697", "GSM2245698", "GSM2245699", "GSM2245700", "GSM2245701", "GSM2245702", "GSM2245703", "GSM2245704", "GSM2245705", "GSM2245706", "GSM2245707", "GSM2245708", "GSM2245709", "GSM2245710", "GSM2245711", "GSM2245712", "GSM2245713", "GSM2245714", "GSM2245715", "GSM2245716", "GSM2245717", "GSM2245718", "GSM2245719", "GSM2245720", "GSM2245721", "GSM2245722", "GSM2245723", "GSM2245724", "GSM2245725", "GSM2245726", "GSM2245727", "GSM2245728", "GSM2245729", "GSM2245730", "GSM2245731", "GSM2245732", "GSM2245733", "GSM2245734", "GSM2245735", "GSM2245736", "GSM2245737", "GSM2245738", "GSM2245739", "GSM2245740", "GSM2245741", "GSM2245742", "GSM2245743", "GSM2245744", "GSM2245745", "GSM2245746", "GSM2245747", "GSM2245748", "GSM2245749", "GSM2245750", "GSM2245751", "GSM2245752", "GSM2245753", "GSM2245754", "GSM2245755", "GSM2245756", "GSM2245757", "GSM2245758", "GSM2245759", "GSM2245760", "GSM2245761", "GSM2245762", "GSM2245763", "GSM2245764", "GSM2245765", "GSM2245766", "GSM2245767", "GSM2245768", "GSM2245769", "GSM2245770", "GSM2245771", "GSM2245772", "GSM2245773", "GSM2245774", "GSM2245775", "GSM2245776", "GSM2245777", "GSM2245778", "GSM2245779", "GSM2245780", "GSM2245781", "GSM2245782", "GSM2245783", "GSM2245784", "GSM2245785", "GSM2245786", "GSM2245787", "GSM2245788", "GSM2245789", "GSM2245790", "GSM2245791", "GSM2245792", "GSM2245793", 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