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pmid:34527340
Screening and evaluation of the role of immune genes of brain metastasis in lung adenocarcinoma progression based on the TCGA and GEO databases.
Cheng Chen · Qiang Guo · Yang Tang · Wendong Qu · Jiebin Zuo · Xixian Ke · Yongxiang Song
Journal of thoracic disease · 2021 doi:10.21037/jtd-21-935
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34527340", "kind": "science-record", "revision": 8, "content_hash": "sha256:e3870111eb1c73093078222bdcf3a603d249732d620172e3e059a4f6ff5b86c7", "created_at": "2026-11-01T15:41:52Z", "updated_at": "2026-11-01T22:04:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and evaluation of the role of immune genes of brain metastasis in lung adenocarcinoma progression based on the TCGA and GEO databases.", "doi": "10.21037/jtd-21-935", "pmid": "34527340", "authors": ["Cheng Chen", "Qiang Guo", "Yang Tang", "Wendong Qu", "Jiebin Zuo", "Xixian Ke", "Yongxiang Song"], "journal": "Journal of thoracic disease", "year": 2021, "abstract": "BACKGROUND: Brain metastasis was one of the factors leading to the poor long-term prognosis of patients with lung adenocarcinoma (LUAD).\nMETHODS: The expression levels of immune genes in LUAD and LUAD brain metastases tissues were analyzed in GSE161116 dataset using the GEO2R, and the levels of differential immune genes in normal lung and LUAD tissues were verified. The biological functions and signaling mechanisms of the differential immune genes were explored via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Cox regression analysis was used to screen the prognostic factors of LUAD patients, and a risk model was constructed. The role of the model was checked in the development of LUAD via receiver operating characteristic analysis, gene set enrichment analysis, and Cox regression analysis.\nRESULTS: Differentially expressed genes (DEGs) in brain metastasis were involved in the adaptive immune response, B cell differentiation, leukocyte migration, NF-kB signaling pathway, among others. The expression levels of TNFRSF11A, MS4A2, IL11, CAMP, MS4A1, and F2RL1 were independent factors affecting the poor prognosis of LUAD patients via Cox regression analysis and Akaike information criterion. In the constructed risk model, the overall survival of LUAD patients in the high-risk group was poor. The risk model was significantly related to the gender, clinical stage, T stage, lymph node metastasis, and survival status of LUAD patients. In addition, the risk model score was an independent risk factor that affected the poor prognosis of LUAD patients. TNFRSF11A, CAMP, F2RL1, IL11, MS4A1, and MS4A2 of the risk factors had diagnostic significance in LUAD brain metastasis and LUAD. The risk model participated in cytokinetic process, cell cycle, citrate cycle TCA cycle, etc. The risk model score was correlated with the levels of B cells memory, mast cells resting, macrophages M0, mast cells activated, neutrophils, eosinophils, T cells gamma delta, and immune cell markers.\nCONCLUSIONS: The risk model based on the LUAD brain metastasis immune factors TNFRSF11A, MS4A2, IL11, CAMP, MS4A1, and F2RL1 was related to the diagnosis, poor prognosis, and immune infiltrating cells of LUAD patients, and is expected to provide a reference for the development of treatment strategies for LUAD patients.", "claims": [{"id": "claim-method", "statement": "K-M survival analysis of the GSE31210 and Jacob-00182-UM datasets showed that the expression levels of TNFRSF11A and MS4A2 were significantly correlated with the OS and relapse free survival (RFS) in LUAD patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34527340", "locator": "sections[17] \"The role of independent prognostic gene expression levels in the progression of LUAD\" paragraph 2", "quote": "K-M survival analysis of the GSE31210 and Jacob-00182-UM datasets showed that the expression levels of TNFRSF11A and MS4A2 were significantly correlated with the OS and relapse free survival (RFS) in LUAD patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "There were 9 LUAD and LUAD brain metastases tissues in the Gene Expression Omnibus (GEO) database GSE161116 dataset (Figure S1A). Among them, there were 10 EGFR mutant and 8 wild-type patients (Figure S1B,C). There were 11 female patients and 7 male patients (Figure S1D). The GEO GSE161116 dataset of 9 LUAD and 9 LUAD brain metastasis samples and GPL19965 annotation information were downloaded, and the expression levels of the prognostic genes were analyzed in LUAD and LUAD brain metastasis tissues by gender and EGFR mutation groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34527340", "locator": "sections[3] \"Differentially expressed immune genes\" paragraph 2", "quote": "There were 9 LUAD and LUAD brain metastases tissues in the Gene Expression Omnibus (GEO) database GSE161116 dataset (Figure S1A)."}, {"asset": "source:pmid:34527340", "locator": "sections[3] \"Differentially expressed immune genes\" paragraph 2", "quote": "Among them, there were 10 EGFR mutant and 8 wild-type patients (Figure S1B,C)."}, {"asset": "source:pmid:34527340", "locator": "sections[3] \"Differentially expressed immune genes\" paragraph 2", "quote": "There were 11 female patients and 7 male patients (Figure S1D)."}, {"asset": "source:pmid:34527340", "locator": "sections[7] \"Identification of independent prognostic genes\" paragraph 2", "quote": "The GEO GSE161116 dataset of 9 LUAD and 9 LUAD brain metastasis samples and GPL19965 annotation information were downloaded, and the expression levels of the prognostic genes were analyzed in LUAD and LUAD brain metastasis tissues by gender and EGFR mutation groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34527340"], "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:GSE13213"], "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:GSE13213"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34527340", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jtd-21-935", "sha256": "sha256:11b054516b958495490c95d27f77a6f87f19b7bfa635c6c2c7180d9b5613251f", "bytes": 38576, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jtd-21-935", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8411151", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13213", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13213", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13213", "version": null, "note": "There were 9 LUAD and LUAD brain metastases tissues in the Gene Expression Omnibus (GEO) database GSE161116 dataset (Figure S1A). Among them, there were 10 EGFR mutant and 8 wild-type patients (Figure S1B,C). There were 11 female patients and 7 male patients (Figure S1D). The GEO GSE161116 dataset of 9 LUAD and 9 LUAD brain metastasis samples and GPL19965 annotation information were downloaded, and the expression levels of the prognostic genes were analyzed in LUAD and LUAD brain metastasis tissues by gender and EGFR mutation groups.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "There were 9 LUAD and LUAD brain metastases tissues in the Gene Expression Omnibus (GEO) database GSE161116 dataset (Figure S1A). Among them, there were 10 EGFR mutant and 8 wild-type patients (Figure S1B,C). There were 11 female patients and 7 male patients (Figure S1D). 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The GEO GSE161116 dataset of 9 LUAD and 9 LUAD brain metastasis samples and GPL19965 annotation information were downloaded, and the expression levels of the prognostic genes were analyzed in LUAD and LUAD brain metastasis tissues by gender and EGFR mutation groups.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4889789", "GSM4889790", "GSM4889791", "GSM4889792", "GSM4889793", "GSM4889794", "GSM4889795", "GSM4889796", "GSM4889797", "GSM4889798", "GSM4889799", "GSM4889800", "GSM4889801", "GSM4889802", "GSM4889803", "GSM4889804", "GSM4889805", "GSM4889806", "GSM4889807", "GSM4889808", "GSM4889809", "GSM4889810", "GSM4889811", "GSM4889812", "GSM4889813", "GSM4889814", "GSM4889815", "GSM4889816"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "19965", "taxon": "Homo sapiens", "title": "Comparative Analysis of the Tumor Immune-Microenvironment of Primary and Brain Metastases of Non-Small-Cell Lung Cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31210", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31210", "version": null, "note": "There were 9 LUAD and LUAD brain metastases tissues in the Gene Expression Omnibus (GEO) database GSE161116 dataset (Figure S1A). Among them, there were 10 EGFR mutant and 8 wild-type patients (Figure S1B,C). There were 11 female patients and 7 male patients (Figure S1D). The GEO GSE161116 dataset of 9 LUAD and 9 LUAD brain metastasis samples and GPL19965 annotation information were downloaded, and the expression levels of the prognostic genes were analyzed in LUAD and LUAD brain metastasis tissues by gender and EGFR mutation groups.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "There were 9 LUAD and LUAD brain metastases tissues in the Gene Expression Omnibus (GEO) database GSE161116 dataset (Figure S1A). Among them, there were 10 EGFR mutant and 8 wild-type patients (Figure S1B,C). There were 11 female patients and 7 male patients (Figure S1D). The GEO GSE161116 dataset of 9 LUAD and 9 LUAD brain metastasis samples and GPL19965 annotation information were downloaded, and the expression levels of the prognostic genes were analyzed in LUAD and LUAD brain metastasis tissues by gender and EGFR mutation groups.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM773540", "GSM773541", "GSM773542", "GSM773543", "GSM773544", "GSM773545", "GSM773546", "GSM773547", "GSM773548", "GSM773549", "GSM773550", "GSM773551", "GSM773552", "GSM773553", "GSM773554", "GSM773555", "GSM773556", "GSM773557", "GSM773558", "GSM773559", "GSM773560", "GSM773561", "GSM773562", "GSM773563", "GSM773564", "GSM773565", "GSM773566", "GSM773567", "GSM773568", "GSM773569", "GSM773570", "GSM773571", "GSM773572", "GSM773573", "GSM773574", "GSM773575", "GSM773576", "GSM773577", "GSM773578", "GSM773579", "GSM773580", "GSM773581", "GSM773582", "GSM773583", "GSM773584", "GSM773585", "GSM773586", "GSM773587", "GSM773588", "GSM773589", 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"media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7df9b657179b985e3b22e8f1138c3893bc9a6da4fe7aba3a6dcc092d3f40c537", "bytes": 2649, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t1", "version": null, "note": "The 97 immune genes of brain metastasis were abnormally expressed in LUAD tissues", "structure": {"pmcid": "PMC8411151", "section_index": 13, "section_title": "Differentially expressed immune genes in LUAD brain metastasis", "row_count": 50, "column_count": 4}, "table": {"label": "Table 1", "caption": "The 97 immune genes of brain metastasis were abnormally expressed in LUAD tissues", "rows": [["Gene", "logFC", "Gene", "logFC"], ["IL5RA", "−1.935544008", "LTA", "1.029192307"], ["CXCL12", "−1.11625871", "C8B", "−2.503444527"], ["SERPING1", "−1.254772313", "THY1", "1.469872699"], ["ENG", "−1.481935175", "PDCD1", "1.124336529"], ["CXCR2", "−2.430598894", "TNFSF12", 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["LILRB3", "−1.209333681", "", ""], ["FCGR3A", "−1.116555199", "ITGAL", "−1.045741499"], ["CXCL13", "1.707906442", "CTSG", "−1.704944547"], ["KLRF1", "−1.416602094", "IL6", "−2.664089273"], ["LCN2", "2.78939134", "IFNG", "1.399852741"], ["TNFRSF17", "1.99794901", "LAG3", "1.413191105"], ["JAM3", "−1.047962968", "BST1", "−1.011723917"], ["TLR4", "−1.37511463", "CAMP", "−2.468673216"], ["CD79A", "1.622713923", "THBD", "−2.304370096"], ["PECAM1", "−2.164796954", "CD19", "1.413990294"], ["CCL18", "−1.039124738", "TLR10", "1.369103797"], ["CDH5", "−2.406255545", "CYBB", "−1.155101404"], ["JAK3", "1.263929458", "MS4A1", "1.112359924"], ["CD27", "1.441085273", "IL7R", "−1.85923146"], ["LTF", "1.438494755", "BTK", "−1.21746455"], ["CD34", "−1.528396601", "CXCL2", "−2.240927179"], ["MS4A2", "−1.69248968", "CFD", "−2.212692861"], ["CCL14", "−2.268425282", "F2RL1", "1.447418839"], ["RRAD", "−1.04531552", "LRRN3", "−2.488365743"], ["CEACAM8", "−1.952591862", "C7", "−1.60908323"], ["TAL1", "−2.625803635", "CFP", "−1.910704296"], ["CMA1", "−1.586930888", "FOS", "−1.547672977"], ["FOXP3", "1.982929634", "C6", "−1.906589961"], ["IL11", "2.914495535", "COL3A1", "2.685880542"], ["CD83", "−1.518456051", "IL34", "−1.129101453"]], "row_count": 50, "column_count": 4, "numeric_cells": 120, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:34527340:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ecf14761e5fd54e7421bce270d62a9e10805b42af231c5688dcd2a6dbea386c", "bytes": 646, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t2", "version": null, "note": "Hub genes of the PPI network", "structure": {"pmcid": "PMC8411151", "section_index": 14, "section_title": "The biological functions, signaling mechanisms, and the PPI network involved in the differentially expressed immune genes of LUAD brain metastasis", "row_count": 11, "column_count": 3}, "table": {"label": "Table 2", "caption": "Hub genes of the PPI network", "rows": [["Name", "Description", "Score"], ["FOXP3", "Forkhead box P3", "6.73E+07"], ["CTLA4", "Cytotoxic T-lymphocyte associated protein 4", "6.72E+07"], ["IL6", "Interleukin 6", "6.68E+07"], ["CD19", "CD19 molecule", "6.64E+07"], ["IFNG", "Interferon gamma", "6.56E+07"], ["CD27", "CD27 molecule", "6.53E+07"], ["PRF1", "Perforin 1", "5.97E+07"], ["IL7R", "Interleukin 7 receptor", "5.34E+07"], ["TNFRSF9", "TNF receptor superfamily member 9", "5.15E+07"], ["TNFSF4", "TNF superfamily member 4", "5.12E+07"]], "row_count": 11, "column_count": 3, "numeric_cells": 20, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:34527340:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:03606526797e2fbbfb9625b8dc89df08bba5778ac206ecd40f0607327bd5d68c", "bytes": 2129, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#t3", "version": null, "note": "Univariate Cox regression analysis showed the influencing genes of the poor prognosis of LUAD patients", "structure": {"pmcid": "PMC8411151", "section_index": 15, "section_title": "Construction of the risk model", "row_count": 29, "column_count": 5}, "table": {"label": "Table 3", "caption": "Univariate Cox regression analysis showed the influencing genes of the poor prognosis of LUAD patients", "rows": [["Gene", "HR", "HR.95L", "HR.95H", "P value"], ["IL5RA", "0.567969541", "0.354788527", "0.909244169", "0.018460133"], ["POU2AF1", "0.845127424", "0.729284998", "0.979370705", "0.02528008"], ["TPSAB1", "0.882145437", "0.784237159", "0.992277097", "0.036696354"], ["LILRB3", "0.693103481", "0.507451451", "0.94667664", "0.021197708"], ["TNFRSF11A", "1.342513034", "1.010304964", "1.783957628", "0.042291011"], ["TNFSF12", 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"0.784427751", "0.613385392", "1.003165229", "0.053017128"], ["MS4A1", "−0.163327726", "0.849312801", "0.730494719", "0.98745715", "0.033660229"], ["F2RL1", "0.177638067", "1.194392953", "1.044013084", "1.366433572", "0.009672824"]], "row_count": 7, "column_count": 6, "numeric_cells": 34, "header_rows": 1, "locator": "section[15]/table-wrap[2]#t4"}}, {"id": "asset:table:pmid:34527340:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fed65fec2a3dcd32fd01673362cbd4309af81dc1147f093558aff9da44ce03a7", "bytes": 1655, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#t5", "version": null, "note": "K-M survival analysis showed that the expression levels of the immune genes were significantly correlated with the OS and PFS in LUAD patients in the PrognoScan database", "structure": {"pmcid": "PMC8411151", "section_index": 17, "section_title": "The role of independent prognostic gene expression levels in the progression of LUAD", "row_count": 15, "column_count": 7}, "table": {"label": "Table 5", "caption": "K-M survival analysis showed that the expression levels of the immune genes were significantly correlated with the OS and PFS in LUAD patients in the PrognoScan database", "rows": [["Gene and dataset", "Prognosis", "Probe ID", "N", "P", "COX P", "HR (95% CI)"], ["TNFRSF11A-GSE31210", "OS", "207037_at", "204", "0.00634647", "0.00898712", "2.38 (1.24–4.55)"], ["TNFRSF11A-GSE31210", "OS", "238846_at", "204", "0.168781", "0.0472737", "1.65 (1.01–2.72)"], ["TNFRSF11A-GSE31210", "RFS", "238846_at", "204", "0.0270956", "0.0154956", "1.60 (1.09–2.34)"], ["TNFRSF11A-GSE31210", "RFS", "207037_at", "204", "0.0180054", "0.0221418", "1.84 (1.09–3.10)"], ["MS4A2-GSE31210", "OS", "207496_at", "204", "0.00987325", "0.00296026", "0.54 (0.36–0.81)"], ["MS4A2-GSE31210", "OS", "207497_s_at", "204", "0.0173826", "0.0307801", "0.58 (0.35–0.95)"], ["MS4A2-Jacob-00182-UM", "OS", "207496_at", "178", "0.086174", "0.0336075", "0.79 (0.63–0.98)"], ["MS4A2-GSE31210", "RFS", "207496_at", "204", "0.00155053", "0.0032846", "0.64 (0.48–0.86)"], ["MS4A1-Jacob-00182-UM", "OS", "210356_x_at", "178", "0.259787", "0.0342218", "0.69 (0.49–0.97)"], ["MS4A1-Jacob-00182-UM", "OS", "217418_x_at", "178", "0.168491", "0.0421624", "0.76 (0.59–0.99)"], ["IL11-Jacob-00182-CANDF", "OS", "206924_at", "82", "–", "0.0146906", "1.96 (1.14–3.36)"], ["IL11-GSE31210", "OS", "206924_at", "204", "0.046182", "0.248705", "1.28 (0.84–1.95)"], ["F2RL1-GSE13213", "OS", "A_23_P58835", "117", "0.0159142", "0.0256215", "1.29 (1.03–1.61)"], ["CAMP-MICHIGAN-LC", "OS", "Z38026_at", "86", "0.00882622", "0.207221", "0.61 (0.28–1.32)"]], "row_count": 15, "column_count": 7, "numeric_cells": 83, "header_rows": 1, "locator": "section[17]/table-wrap[1]#t5"}}, {"id": "asset:table:pmid:34527340:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5240cd235b6041bf03e667001956ae91b606916ef32c6704c7f1ad917939cb13", "bytes": 2254, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#t6", "version": null, "note": "The risk score was significantly correlated with the levels of LUAD immune cell markers", "structure": {"pmcid": "PMC8411151", "section_index": 19, "section_title": "The risk model was related to the LUAD immune microenvironment", "row_count": 96, "column_count": 2}, "table": {"label": "Table 6", "caption": "The risk score was significantly correlated with the levels of LUAD immune cell markers", "rows": [["Gene", "Cor"], ["XCL1", "−0.162"], ["CSF1R", "−0.254"], ["CCR5", "−0.317"], ["CXCL12", "−0.284"], ["CCL3", "−0.13"], ["PVR", "0.332"], ["CCL7", "0.135"], ["CXCR2", "−0.157"], ["IL6R", "−0.231"], ["CCL17", "−0.257"], ["CXCR4", "−0.377"], ["TIGIT", "−0.343"], ["CD244", "−0.309"], ["NT5E", "0.121"], ["CD48", "−0.469"], ["TNFSF14", "−0.226"], ["HAVCR2", "−0.248"], ["CCL2", "−0.114"], ["CCL19", "−0.453"], ["CD80", "−0.22"], ["CD276", "0.282"], ["CXCR3", "−0.312"], ["CD86", "−0.254"], ["TNFRSF25", "−0.26"], ["HLA-DRB1", "−0.383"], ["HLA-DQA1", "−0.393"], ["HLA-DQB1", "−0.323"], ["HLA-DMB", "−0.414"], ["HLA-DPB1", "−0.431"], ["CCL22", "−0.206"], ["PDCD1LG2", "−0.174"], ["TNFRSF18", "−0.133"], ["TNFRSF4", "−0.225"], ["TNFRSF14", "−0.29"], ["TNFSF13B", "−0.309"], ["HLA-DPA1", "−0.391"], ["TNFRSF13C", "−0.467"], ["TNFRSF9", "−0.126"], ["CTLA4", "−0.337"], ["PDCD1", "−0.28"], ["CXCR6", "−0.329"], ["CCL21", "−0.134"], ["CCL23", "−0.301"], ["CXCL9", "−0.205"], ["CCR2", "−0.372"], ["HLA-B", "−0.225"], ["CCR1", "−0.22"], ["CCL4", "−0.199"], ["CXCL10", "−0.111"], ["CCR4", "−0.422"], ["LTA", "−0.417"], ["CCR7", "−0.476"], ["ENTPD1", "−0.249"], ["BTLA", "−0.418"], ["CXCL13", "−0.368"], ["XCL2", "−0.266"], ["HLA-E", "−0.307"], ["TNFSF15", "−0.146"], ["TNFRSF17", "−0.368"], ["TNFSF13", "−0.171"], ["CX3CR1", "−0.253"], ["TMEM173", "−0.257"], ["IL10", "−0.295"], ["HLA-C", "−0.183"], ["CXCL8", "0.186"], ["HLA-DMA", "−0.433"], ["CCL18", "−0.263"], ["TGFBR1", "0.111"], ["CD27", "−0.421"], ["CCL26", "0.146"], ["TNFSF9", "0.101"], ["HLA-DQA2", "−0.222"], ["CD40", "−0.221"], ["HLA-DOB", "−0.467"], ["CCR8", "−0.222"], ["HLA-DRA", "−0.398"], ["CCL13", "−0.133"], ["IDO1", "−0.157"], ["ICOS", "−0.341"], ["HLA-F", "−0.235"], ["CD96", "−0.371"], ["LAG3", "−0.235"], ["TNFRSF8", "−0.107"], ["CXCL14", "−0.18"], ["B2M", "−0.182"], ["LGALS9", "−0.182"], ["IL2RA", "−0.133"], ["CXCL2", "−0.144"], ["CXCL17", "−0.32"], ["CD28", "−0.357"], ["HLA-DOA", "−0.42"], ["TAPBP", "−0.11"], ["CXCL5", "0.213"], ["CX3CL1", "−0.163"], ["HLA-A", "−0.159"]], "row_count": 96, "column_count": 2, "numeric_cells": 128, "header_rows": 1, "locator": "section[19]/table-wrap[1]#t6"}}], "gaps": ["asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE13213 licence not read", 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analysis of the GSE31210 and Jacob-00182-UM datasets showed that the expression levels of TNFRSF11A and MS4A2 were significantly correlated with the OS and relapse free survival (RFS) in LUAD patients."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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