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pmid:36561844
Integrated bioinformatics analysis shows integrin alpha 3 is a prognostic biomarker for pancreatic cancer.
Fangfang Hu · Liangtao Zhao · Yang Wang · Hao Ye · Haodong Tang · Jiahua Zhou
Open medicine (Warsaw, Poland) · 2022 doi:10.1515/med-2022-0606
Paper
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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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The ITGA3 gene expression data were extracted from The Cancer Genome Atlas (TCGA) pancreatic adenocarcinoma (PAAD) cohort and 14 Gene Expression Omnibus microarray datasets. The differences in ITGA3 expression levels between tumor and non-tumor tissues were compared using the Mann-Whitney U test. Cox regression analysis and meta-analysis were performed to detect the association of ITGA3 expression with PCa prognosis. ITGA3 expression was higher in tumors than in controls. Tumors with advanced grades (3/4) had higher ITGA3 levels compared with early-grade tumors (1/2). The meta-analysis of the TCGA PAAD cohort and seven microarray datasets (GSE28735, GSE62452, GSE79668, GSE71729, GSE57495, GSE78229, and GSE21501) showed that ITGA3 was a prognostic biomarker in PCa (hazard ratio (HR) = 1.38, 95% confidence interval (CI) 1.26-1.51, p < 0.00001). Five ITGA3-related genes, including ITGB1 (HR = 1.6), ITGB5 (HR = 1.6), ITGB6 (HR = 1.6), LAMA3 (HR = 2.1), and CD9 (HR = 2.3), correlated with PCa prognosis significantly (p < 0.05). Functional enrichment analysis showed that ITGA3 was related to \"hsa04151: PI3K-Akt signaling pathway\" and \"hsa04510: Focal adhesion.\" We concluded that high ITGA3 expression was a potential prognostic biomarker in PCa.", "claims": [{"id": "claim-method", "statement": "Cox regression analysis and meta-analysis were performed to detect the association of ITGA3 expression with PCa prognosis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36561844", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Cox regression analysis and meta-analysis were performed to detect the association of ITGA3 expression with PCa prognosis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). 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The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM563305", "GSM563306", "GSM563307", "GSM563308", "GSM563309", "GSM563310", "GSM563311", "GSM563312", "GSM563313", "GSM563314", "GSM563315", "GSM563316", "GSM563317", "GSM563318", "GSM563319", "GSM563320"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Affymetrix Arrays Interrogated with Tumor/Normal Pancreatic Samples", "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:GSE28735", "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=GSE28735", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28735", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM711904", "GSM711905", "GSM711906", "GSM711907", "GSM711908", "GSM711909", "GSM711910", "GSM711911", "GSM711912", "GSM711913", "GSM711914", "GSM711915", "GSM711916", "GSM711917", "GSM711918", "GSM711919", "GSM711920", "GSM711921", "GSM711922", "GSM711923", "GSM711924", "GSM711925", "GSM711926", "GSM711927", "GSM711928", "GSM711929", "GSM711930", "GSM711931", "GSM711932", "GSM711933", "GSM711934", "GSM711935", "GSM711936", "GSM711937", "GSM711938", "GSM711939", "GSM711940", "GSM711941", "GSM711942", "GSM711943", "GSM711944", "GSM711945", "GSM711946", "GSM711947", "GSM711948", "GSM711949", "GSM711950", "GSM711951", "GSM711952", "GSM711953", "GSM711954", "GSM711955", "GSM711956", "GSM711957", "GSM711958", "GSM711959", "GSM711960", "GSM711961", "GSM711962", "GSM711963", "GSM711964", "GSM711965", "GSM711966", "GSM711967", "GSM711968", "GSM711969", "GSM711970", "GSM711971", "GSM711972", "GSM711973", "GSM711974", "GSM711975", "GSM711976", "GSM711977", "GSM711978", "GSM711979", "GSM711980", "GSM711981", "GSM711982", "GSM711983", "GSM711984", "GSM711985", "GSM711986", "GSM711987", "GSM711988", "GSM711989", "GSM711990", "GSM711991", "GSM711992", "GSM711993"], "sample_count": 90, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues from 45 patients with pancreatic ductal adenocarcinoma", "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:GSE32676", "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=GSE32676", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32676", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM811004", "GSM811005", "GSM811006", "GSM811007", "GSM811008", "GSM811009", "GSM811010", "GSM811011", "GSM811012", "GSM811013", "GSM811014", "GSM811015", "GSM811016", "GSM811017", "GSM811018", "GSM811019", "GSM811020", "GSM811021", "GSM811022", "GSM811023", "GSM811024", "GSM811025", "GSM811026", "GSM811027", "GSM811028", "GSM811029", "GSM811030", "GSM811031", "GSM811032", "GSM811033", "GSM811034", "GSM811035"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Integrative Survival-Based Molecular Profiling of Human Pancreatic Cancer [mRNA]", "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:GSE41372", "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=GSE41372", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41372", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1015732", "GSM1015733", "GSM1015734", "GSM1015735", "GSM1015736", "GSM1015737", "GSM1015738", "GSM1015739", "GSM1015740", "GSM1015741", "GSM1015742", "GSM1015743", "GSM1015744", "GSM1015745", "GSM1015746", "GSM1015747", "GSM1015748", "GSM1015749", "GSM1015750", "GSM1015751", "GSM1015752", "GSM1015753", "GSM1015754", "GSM1015755", "GSM1015756", "GSM1015757", "GSM1015758", "GSM1015759", "GSM1015760", "GSM1015761"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "16142;6244", "taxon": "Homo sapiens", "title": "MicroRNAs Cooperatively Inhibit a Network of Tumor Suppressor Genes to Promote Pancreatic Tumor Growth and Progression", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE57495", "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=GSE57495", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57495", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1383778", "GSM1383779", "GSM1383780", "GSM1383781", "GSM1383782", "GSM1383783", "GSM1383784", "GSM1383785", "GSM1383786", "GSM1383787", "GSM1383788", "GSM1383789", "GSM1383790", "GSM1383791", "GSM1383792", "GSM1383793", "GSM1383794", "GSM1383795", "GSM1383796", "GSM1383797", "GSM1383798", "GSM1383799", "GSM1383800", "GSM1383801", "GSM1383802", "GSM1383803", "GSM1383804", "GSM1383805", "GSM1383806", "GSM1383807", "GSM1383808", "GSM1383809", "GSM1383810", "GSM1383811", "GSM1383812", "GSM1383813", "GSM1383814", "GSM1383815", "GSM1383816", "GSM1383817", "GSM1383818", "GSM1383819", "GSM1383820", "GSM1383821", "GSM1383822", "GSM1383823", "GSM1383824", "GSM1383825", "GSM1383826", "GSM1383827", "GSM1383828", "GSM1383829", "GSM1383830", "GSM1383831", "GSM1383832", "GSM1383833", "GSM1383834", "GSM1383835", "GSM1383836", "GSM1383837", "GSM1383838", "GSM1383839", "GSM1383840"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "Development of a prognostic gene signature in pancreatic 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:GSE62452", "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=GSE62452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62452", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1527105", "GSM1527106", "GSM1527107", "GSM1527108", "GSM1527109", "GSM1527110", "GSM1527111", "GSM1527112", "GSM1527113", "GSM1527114", "GSM1527115", "GSM1527116", "GSM1527117", "GSM1527118", "GSM1527119", "GSM1527120", "GSM1527121", "GSM1527122", "GSM1527123", "GSM1527124", "GSM1527125", "GSM1527126", "GSM1527127", "GSM1527128", "GSM1527129", "GSM1527130", "GSM1527131", "GSM1527132", "GSM1527133", "GSM1527134", "GSM1527135", "GSM1527136", "GSM1527137", "GSM1527138", "GSM1527139", "GSM1527140", "GSM1527141", "GSM1527142", "GSM1527143", "GSM1527144", "GSM1527145", "GSM1527146", "GSM1527147", "GSM1527148", "GSM1527149", "GSM1527150", "GSM1527151", "GSM1527152", "GSM1527153", "GSM1527154", "GSM1527155", "GSM1527156", "GSM1527157", "GSM1527158", "GSM1527159", "GSM1527160", "GSM1527161", "GSM1527162", "GSM1527163", "GSM1527164", "GSM1527165", "GSM1527166", "GSM1527167", "GSM1527168", "GSM1527169", "GSM1527170", "GSM1527171", "GSM1527172", "GSM1527173", "GSM1527174", "GSM1527175", "GSM1527176", "GSM1527177", "GSM1527178", "GSM1527179", "GSM1527180", "GSM1527181", "GSM1527182", "GSM1527183", "GSM1527184", "GSM1527185", "GSM1527186", "GSM1527187", "GSM1527188", "GSM1527189", "GSM1527190", "GSM1527191", "GSM1527192", "GSM1527193", "GSM1527194", "GSM1527195", "GSM1527196", "GSM1527197", "GSM1527198", "GSM1527199", "GSM1527200", "GSM1527201", "GSM1527202", "GSM1527203", "GSM1527204", "GSM1527205", "GSM1527206", "GSM1527207", "GSM1527208", "GSM1527209", "GSM1527210", "GSM1527211", "GSM1527212", "GSM1527213", "GSM1527214", "GSM1527215", "GSM1527216", "GSM1527217", "GSM1527218", "GSM1527219", "GSM1527220", "GSM1527221", "GSM1527222", "GSM1527223", "GSM1527224", "GSM1527225", "GSM1527226", "GSM1527227", "GSM1527228", "GSM1527229", "GSM1527230", "GSM1527231", "GSM1527232", "GSM1527233", "GSM1527234"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 69 pancreatic tumors and 61 adjacent non-tumor tissue from patients with pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE71729", "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=GSE71729", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71729", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). 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The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1527105", "GSM1527109", "GSM1527137", "GSM1527139", "GSM1527141", "GSM1527145", "GSM1527147", "GSM1527149", "GSM1527151", "GSM1527153", "GSM1527155", "GSM1527157", "GSM1527159", "GSM1527161", "GSM1527163", "GSM1527165", "GSM1527167", "GSM1527169", "GSM1527171", "GSM1527175", "GSM1527177", "GSM1527179", "GSM1527181", "GSM1527183", "GSM1527185", "GSM1527189", "GSM1527191", "GSM1527193", "GSM1527196", "GSM1527198", "GSM1527199", "GSM1527200", "GSM1527202", "GSM1527204", "GSM1527205", "GSM1527207", "GSM1527209", "GSM1527212", "GSM1527213", "GSM1527215", "GSM1527216", "GSM1527218", "GSM1527219", "GSM1527220", "GSM1527223", "GSM1527225", "GSM1527227", "GSM1527228", "GSM1527230", "GSM1527232"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 50 pancreatic tumors tissue from patients with pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE79668", "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=GSE79668", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE79668", "version": null, "note": "Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). 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The 14 microarray datasets GSE16515, GSE22780, GSE15471, GSE71989, GSE32676, GSE15932, GSE41372, GSE28735, GSE62452, GSE79668, GSE57495, GSE78229, GSE71729, and GSE21501 were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2100851", "GSM2100852", "GSM2100853", "GSM2100854", "GSM2100855", "GSM2100856", "GSM2100857", "GSM2100858", "GSM2100859", "GSM2100860", "GSM2100861", "GSM2100862", "GSM2100863", "GSM2100864", "GSM2100865", "GSM2100866", "GSM2100867", "GSM2100868", "GSM2100869", "GSM2100870", "GSM2100871", "GSM2100872", "GSM2100873", "GSM2100874", "GSM2100875", "GSM2100876", "GSM2100877", "GSM2100878", "GSM2100879", "GSM2100880", "GSM2100881", "GSM2100882", "GSM2100883", "GSM2100884", "GSM2100885", "GSM2100886", "GSM2100887", "GSM2100888", "GSM2100889", "GSM2100890", "GSM2100891", "GSM2100892", "GSM2100893", "GSM2100894", "GSM2100895", "GSM2100896", "GSM2100897", "GSM2100898", "GSM2100899", "GSM2100900", "GSM2100901"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "RNA-sequencing of human pancreatic adenocarcinoma cancer tissues", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE15471 not downloaded", "asset:data:geo:GSE15471 licence not read", "asset:data:geo:GSE15932 not downloaded", "asset:data:geo:GSE15932 licence not read", "asset:data:geo:GSE16515 not downloaded", "asset:data:geo:GSE16515 licence not read", "asset:data:geo:GSE21501 not downloaded", "asset:data:geo:GSE21501 licence not read", "asset:data:geo:GSE22780 not downloaded", "asset:data:geo:GSE22780 licence not read", "asset:data:geo:GSE28735 not downloaded", "asset:data:geo:GSE28735 licence not read", "asset:data:geo:GSE32676 not downloaded", "asset:data:geo:GSE32676 licence not read", "asset:data:geo:GSE41372 not downloaded", "asset:data:geo:GSE41372 licence not read", "asset:data:geo:GSE57495 not downloaded", "asset:data:geo:GSE57495 licence not read", "asset:data:geo:GSE62452 not downloaded", "asset:data:geo:GSE62452 licence not read", "asset:data:geo:GSE71729 not downloaded", "asset:data:geo:GSE71729 licence not read", "asset:data:geo:GSE71989 not downloaded", "asset:data:geo:GSE71989 licence not read", "asset:data:geo:GSE78229 not downloaded", "asset:data:geo:GSE78229 licence not read", "asset:data:geo:GSE79668 not downloaded", "asset:data:geo:GSE79668 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Cox regression analysis and meta-analysis were performed to detect the association of ITGA3 expression with PCa prognosis."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.7, "band": "medium", "quote": "Mann-Whitney"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-hazard-ratio", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 1.38, "unit": "hazard ratio", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 1e-05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE16515", "GSE22780", "GSE15471", "GSE71989", "GSE32676", "GSE15932", "GSE41372", "GSE28735", "GSE62452", "GSE79668", "GSE71729", "GSE57495", "GSE78229", "GSE21501"], "resolved_accessions": ["GSE16515", "GSE22780", "GSE15471", "GSE71989", "GSE32676", "GSE15932", "GSE41372", "GSE28735", "GSE62452", "GSE79668", "GSE71729", "GSE57495", "GSE78229", "GSE21501"], "statements": ["Data availability statement: The gene expression RNA-seq in the cohort of GDC TCGA PAAD was extracted from the UCSC Xena (https://xenabrowser.net/datapages/). 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