← All .science files
pmid:33193373
A Novel Signature of 23 Immunity-Related Gene Pairs Is Prognostic of Cutaneous Melanoma.
Ya-Nan Xue · Yi-Nan Xue · Zheng-Cai Wang · Yong-Zhen Mo · Pin-Yan Wang · Wei-Qiang Tan
Frontiers in immunology · 2020 doi:10.3389/fimmu.2020.576914
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 57 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 141 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 214 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[21] array · 7 items
[22] array · 7 items
[23] array · 7 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 37 items
[0] array · 3 items
[1] array · 1 item
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 1 item
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 1 item
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 1 item
[20] array · 7 items
[21] array · 7 items
[22] array · 7 items
[23] array · 7 items
[24] array · 7 items
[25] array · 1 item
[26] array · 7 items
[27] array · 7 items
[28] array · 7 items
[29] array · 7 items
[30] array · 7 items
[31] array · 1 item
[32] array · 7 items
[33] array · 7 items
[34] array · 7 items
[35] array · 7 items
[36] array · 7 items
gaps array · 6 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 3 items
resolved_accessions array · 3 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 10 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[2] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33193373", "kind": "science-record", "revision": 7, "content_hash": "sha256:79681ab1bb2527c7e6635ee8a9f1d2ad774b3a03d4f5702a73cf65eb581ad62c", "created_at": "2026-11-01T15:41:16Z", "updated_at": "2026-11-01T22:02:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Novel Signature of 23 Immunity-Related Gene Pairs Is Prognostic of Cutaneous Melanoma.", "doi": "10.3389/fimmu.2020.576914", "pmid": "33193373", "authors": ["Ya-Nan Xue", "Yi-Nan Xue", "Zheng-Cai Wang", "Yong-Zhen Mo", "Pin-Yan Wang", "Wei-Qiang Tan"], "journal": "Frontiers in immunology", "year": 2020, "abstract": "In this study, we aimed to identify an immune-related signature for predicting prognosis in cutaneous melanoma (CM). Sample data from The Cancer Genome Atlas (TCGA; n = 460) were used to develop a prognostic signature with 23 immune-related gene pairs (23 IRGPs) for CM. Patients were divided into high- and low-risk groups using the TCGA and validation datasets GSE65904 (n = 214), GSE59455 (n = 141), and GSE22153 (n = 79). The ability of the 23-IRGP signature to predict CM was precise, with the stratified high-risk groups showing a poor prognosis, and it had a significant predictive power when used for immune microenvironment and biological analyses. We subsequently established a novel promising prognostic model in CM to determine the association between the immune microenvironment and CM patient results. This approach may be used to discover signatures in other diseases while avoiding the technical biases associated with other platforms.", "claims": [{"id": "claim-method", "statement": "Based on the results of a log-rank test, IRGPs with a false discovery rate (FDR) <0.001 (n = 23) were retained and entered into a least absolute shrinkage and selection operator (LASSO) penalized Cox regression model (iterations = 1000).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33193373", "locator": "sections[5] \"Establishment of Prognostic IRGPs Based on the TCGA Dataset\" paragraph 2", "quote": "Based on the results of a log-rank test, IRGPs with a false discovery rate (FDR) <0.001 (n = 23) were retained and entered into a least absolute shrinkage and selection operator (LASSO) penalized Cox regression model (iterations = 1000)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33193373", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153."}], "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:33193373"], "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:GSE22153"], "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:GSE22153"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33193373", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2020.576914", "sha256": "sha256:53c9d63d4e928198fc903718e1ab14c0c7987cd44705e14549339a93431e3afd", "bytes": 61852, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2020.576914", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7604355", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22153", "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=GSE22153", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22153", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM550966", "GSM550967", "GSM550968", "GSM550969", "GSM550970", "GSM550971", "GSM550972", "GSM550973", "GSM550974", "GSM550975", "GSM550976", "GSM550977", "GSM550978", "GSM550979", "GSM550980", "GSM550981", "GSM550982", "GSM550983", "GSM550984", "GSM550985", "GSM550986", "GSM550987", "GSM550988", "GSM550989", "GSM550990", "GSM550991", "GSM550992", "GSM550993", "GSM550994", "GSM550995", "GSM550996", "GSM550997", "GSM550998", "GSM550999", "GSM551000", "GSM551001", "GSM551002", "GSM551003", "GSM551004", "GSM551005", "GSM551006", "GSM551007", "GSM551008", "GSM551009", "GSM551010", "GSM551011", "GSM551012", "GSM551013", "GSM551014", "GSM551015", "GSM551016", "GSM551017", "GSM551018", "GSM551019", "GSM551020", "GSM551021", "GSM551022"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "6102", "taxon": "Homo sapiens", "title": "Gene Experssion Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome (test set)", "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:GSE59455", "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=GSE59455", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59455", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1437254", "GSM1437255", "GSM1437256", "GSM1437257", "GSM1437258", "GSM1437259", "GSM1437260", "GSM1437261", "GSM1437262", "GSM1437263", "GSM1437264", "GSM1437265", "GSM1437266", "GSM1437267", "GSM1437268", "GSM1437269", "GSM1437270", "GSM1437271", "GSM1437272", "GSM1437273", "GSM1437274", "GSM1437275", "GSM1437276", "GSM1437277", "GSM1437278", "GSM1437279", "GSM1437280", "GSM1437281", "GSM1437282", "GSM1437283", "GSM1437284", "GSM1437285", "GSM1437286", "GSM1437287", "GSM1437288", "GSM1437289", "GSM1437290", "GSM1437291", "GSM1437292", "GSM1437293", "GSM1437294", "GSM1437295", "GSM1437296", "GSM1437297", "GSM1437298", "GSM1437299", "GSM1437300", "GSM1437301", "GSM1437302", "GSM1437303", "GSM1437304", "GSM1437305", "GSM1437306", "GSM1437307", "GSM1437308", "GSM1437309", "GSM1437310", "GSM1437311", "GSM1437312", "GSM1437313", "GSM1437314", "GSM1437315", "GSM1437316", "GSM1437317", "GSM1437318", "GSM1437319", "GSM1437320", "GSM1437321", "GSM1437322", "GSM1437323", "GSM1437324", "GSM1437325", "GSM1437326", "GSM1437327", "GSM1437328", "GSM1437329", "GSM1437330", "GSM1437331", "GSM1437332", "GSM1437333", "GSM1437334", "GSM1437335", "GSM1437336", "GSM1437337", "GSM1437338", "GSM1437339", "GSM1437340", "GSM1437341", "GSM1437342", "GSM1437343", "GSM1437344", "GSM1437345", "GSM1437346", "GSM1437347", "GSM1437348", "GSM1437349", "GSM1437350", "GSM1437351", "GSM1437352", "GSM1437353", "GSM1437354", "GSM1437355", "GSM1437356", "GSM1437357", "GSM1437358", "GSM1437359", "GSM1437360", "GSM1437361", "GSM1437362", "GSM1437363", "GSM1437364", "GSM1437365", "GSM1437366", "GSM1437367", "GSM1437368", "GSM1437369", "GSM1437370", "GSM1437371", "GSM1437372", "GSM1437373", "GSM1437374", "GSM1437375", "GSM1437376", "GSM1437377", "GSM1437378", "GSM1437379", "GSM1437380", "GSM1437381", "GSM1437382", "GSM1437383", "GSM1437384", "GSM1437385", "GSM1437386", "GSM1437387", "GSM1437388", "GSM1437389", "GSM1437390", "GSM1437391", "GSM1437392", "GSM1437393", "GSM1437394"], "sample_count": 141, "group_sizes": null, "group_sizes_basis": null, "platform": "8432", "taxon": "Homo sapiens", "title": "Whole genome expression data from formalin-fixed parrafin embedded (FFPE) primary and metastatic melanomas", "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:GSE65904", "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=GSE65904", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65904", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1608593", "GSM1608594", "GSM1608595", "GSM1608596", "GSM1608597", "GSM1608598", "GSM1608599", "GSM1608600", "GSM1608601", "GSM1608602", "GSM1608603", "GSM1608604", "GSM1608605", "GSM1608606", "GSM1608607", "GSM1608608", "GSM1608609", "GSM1608610", "GSM1608611", "GSM1608612", "GSM1608613", "GSM1608614", "GSM1608615", "GSM1608616", "GSM1608617", "GSM1608618", "GSM1608619", "GSM1608620", "GSM1608621", "GSM1608622", "GSM1608623", "GSM1608624", "GSM1608625", "GSM1608626", "GSM1608627", "GSM1608628", "GSM1608629", "GSM1608630", "GSM1608631", "GSM1608632", "GSM1608633", "GSM1608634", "GSM1608635", "GSM1608636", "GSM1608637", "GSM1608638", "GSM1608639", "GSM1608640", "GSM1608641", "GSM1608642", "GSM1608643", "GSM1608644", "GSM1608645", "GSM1608646", "GSM1608647", "GSM1608648", "GSM1608649", "GSM1608650", "GSM1608651", "GSM1608652", "GSM1608653", "GSM1608654", "GSM1608655", "GSM1608656", "GSM1608657", "GSM1608658", "GSM1608659", "GSM1608660", "GSM1608661", "GSM1608662", "GSM1608663", "GSM1608664", "GSM1608665", "GSM1608666", "GSM1608667", "GSM1608668", "GSM1608669", "GSM1608670", "GSM1608671", "GSM1608672", "GSM1608673", "GSM1608674", "GSM1608675", "GSM1608676", "GSM1608677", "GSM1608678", "GSM1608679", "GSM1608680", "GSM1608681", "GSM1608682", "GSM1608683", "GSM1608684", "GSM1608685", "GSM1608686", "GSM1608687", "GSM1608688", "GSM1608689", "GSM1608690", "GSM1608691", "GSM1608692", "GSM1608693", "GSM1608694", "GSM1608695", "GSM1608696", "GSM1608697", "GSM1608698", "GSM1608699", "GSM1608700", "GSM1608701", "GSM1608702", "GSM1608703", "GSM1608704", "GSM1608705", "GSM1608706", "GSM1608707", "GSM1608708", "GSM1608709", "GSM1608710", "GSM1608711", "GSM1608712", "GSM1608713", "GSM1608714", "GSM1608715", "GSM1608716", "GSM1608717", "GSM1608718", "GSM1608719", "GSM1608720", "GSM1608721", "GSM1608722", "GSM1608723", "GSM1608724", "GSM1608725", "GSM1608726", "GSM1608727", "GSM1608728", "GSM1608729", "GSM1608730", "GSM1608731", "GSM1608732", "GSM1608733", "GSM1608734", "GSM1608735", "GSM1608736", "GSM1608737", "GSM1608738", "GSM1608739", "GSM1608740", "GSM1608741", "GSM1608742", "GSM1608743", "GSM1608744", "GSM1608745", "GSM1608746", "GSM1608747", "GSM1608748", "GSM1608749", "GSM1608750", "GSM1608751", "GSM1608752", "GSM1608753", "GSM1608754", "GSM1608755", "GSM1608756", "GSM1608757", "GSM1608758", "GSM1608759", "GSM1608760", "GSM1608761", "GSM1608762", "GSM1608763", "GSM1608764", "GSM1608765", "GSM1608766", "GSM1608767", "GSM1608768", "GSM1608769", "GSM1608770", "GSM1608771", "GSM1608772", "GSM1608773", "GSM1608774", "GSM1608775", "GSM1608776", "GSM1608777", "GSM1608778", "GSM1608779", "GSM1608780", "GSM1608781", "GSM1608782", "GSM1608783", "GSM1608784", "GSM1608785", "GSM1608786", "GSM1608787", "GSM1608788", "GSM1608789", "GSM1608790", "GSM1608791", "GSM1608792", "GSM1608793", "GSM1608794", "GSM1608795", "GSM1608796", "GSM1608797", "GSM1608798", "GSM1608799", "GSM1608800", "GSM1608801", "GSM1608802", "GSM1608803", "GSM1608804", "GSM1608805", "GSM1608806"], "sample_count": 214, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Whole-genome expression analysis of melanoma tumor biopsies from a population-based cohort.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33193373:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:910578b3debe46877117ea90e133d7d7cc8bf6550fdf206c1cdd7a051e078da5", "bytes": 4228, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T1", "version": null, "note": "Information on the 23-IRGP.", "structure": {"pmcid": "PMC7604355", "section_index": 11, "section_title": "Establishment, Definition, and Genetic Variation of the IRGP Signature", "row_count": 24, "column_count": 7}, "table": {"label": "Table 1", "caption": "Information on the 23-IRGP.", "rows": [["Gene Pair1", "Full Name", "Immune Processes", "Gene Pair2", "Full Name", "Immune Processes", "Coefficient"], ["CD8A", "CD8a molecule", "Antigen_Processing_and_Presentation, Antimicrobials, TCRsignalingPathway", "LTBP2", "latent transforming growth factor beta binding protein 2", "Cytokines", "−0.009639653"], ["HSPA1A", "heat shock 70kDa protein 1A", "Antigen_Processing_and_Presentation", "LYZ", "lysozyme (renal amyloidosis)", "Antimicrobials", "0.098898359"], ["HSPA1A", "heat shock 70kDa protein 1A", "Antigen_Processing_and_Presentation", "GBP2", "guanylate binding protein 2, interferon-inducible", "Antimicrobials", "0.06573857"], ["HSPA1A", "heat shock 70kDa protein 1A", "Antigen_Processing_and_Presentation", "LTBP3", "latent transforming growth factor beta binding protein 3", "Cytokines", "0.00106882"], ["ICAM1", "intercellular adhesion molecule 1", "Antigen_Processing_and_Presentation, NaturalKiller_Cell_Cytotoxicity", "PLXNB2", "plexin B2", "Chemokine_Receptors, Cytokine_Receptors", "-0.039340917"], ["PSME1", "proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)", "Antigen_Processing_and_Presentation", "NENF", "neuron derived neurotrophic factor", "Cytokines", "−0.008677831"], ["ZC3HAV1L", "zinc finger CCCH-type, antiviral 1-like", "Antimicrobials", "CMTM8", "CKLF-like MARVEL transmembrane domain containing 8", "Cytokines", "0.037052249"], ["APOBEC3G", "apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G", "Antimicrobials", "IKBKE", "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon", "Antimicrobials", "-0.511310011"], ["CYBB", "cytochrome b-245, beta polypeptide", "Antimicrobials", "SEMA7A", "semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)", "Chemokines, Cytokines", "−0.0389128"], ["TRIM5", "tripartite motif-containing 5", "Antimicrobials", "SOS1", "son of sevenless homolog 1 (Drosophila)", "NaturalKiller_Cell_Cytotoxicity, TCRsignalingPathway", "−0.064111635"], ["TNFSF10", "tumor necrosis factor (ligand) superfamily, member 10", "Antimicrobials, Cytokines, NaturalKiller_Cell_Cytotoxicity, TNF_Family_Members", "STC1", "stanniocalcin 1", "Cytokines", "−0.089600117"], ["RNASEL", "ribonuclease L (2’,5’-oligoisoadenylate synthetase-dependent)", "Antimicrobials", "TRIM22", "tripartite motif-containing 22", "Antimicrobials", "0.019575179"], ["RARRES3", "retinoic acid receptor responder (tazarotene induced) 3", "Antimicrobials", "DDX17", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17", "Antimicrobials", "−0.036983795"], ["CD40", "CD40 molecule, TNF receptor superfamily member 5", "Antimicrobials, Cytokine_Receptors", "BIRC5", "baculoviral IAP repeat-containing 5", "Antimicrobials", "−0.008823763"], ["ISG15", "ISG15 ubiquitin-like modifier", "Antimicrobials", "NENF", "neuron derived neurotrophic factor", "Cytokines", "−0.225283963"], ["GNLY", "granulysin", "Antimicrobials", "EDNRA", "endothelin receptor type A", "Chemokine_Receptors, Cytokine_Receptors", "−0.027334821"], ["IRF7", "interferon regulatory factor 7", "Antimicrobials", "AKT1", "v-akt murine thymoma viral oncogene homolog 1", "BCRSignalingPathway, TCRsignalingPathway", "−0.035142572"], ["TRIM22", "tripartite motif-containing 22", "Antimicrobials", "CCL17", "chemokine (C-C motif) ligand 17", "Antimicrobials, Chemokines, Cytokines", "−0.270054236"], ["BIRC5", "baculoviral IAP repeat-containing 5", "Antimicrobials", "NGFR", "nerve growth factor receptor (TNFR superfamily, member 16)", "Cytokine_Receptors", "0.211653036"], ["GBP2", "guanylate binding protein 2, interferon-inducible", "Antimicrobials", "PLXNA1", "plexin A1", "Chemokine_Receptors, Cytokine_Receptors", "−0.031264198"], ["GBP2", "guanylate binding protein 2, interferon-inducible", "Antimicrobials", "SHC4", "SHC (Src homology 2 domain containing) family, member 4", "NaturalKiller_Cell_Cytotoxicity", "−0.09011139"], ["PTK2B", "PTK2B protein tyrosine kinase 2 beta", "Antimicrobials, NaturalKiller_Cell_Cytotoxicity", "LHB", "luteinizing hormone beta polypeptide", "Cytokines", "−0.397220258"], ["CD86", "CD86 molecule", "Antimicrobials", "IL1RN", "interleukin 1 receptor antagonist", "Cytokines, Interleukins", "−0.018374851"]], "row_count": 24, "column_count": 7, "numeric_cells": 67, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33193373:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e0abcd7b510ce18339ea4419ff2f5b959dfc7e88232af23f2af4b577b46e7314", "bytes": 2565, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T2", "version": null, "note": "Univariate Cox and Multivariate Cox analysis of clinicopathological factors and risk signatures.", "structure": {"pmcid": "PMC7604355", "section_index": 11, "section_title": "Establishment, Definition, and Genetic Variation of the IRGP Signature", "row_count": 37, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariate Cox and Multivariate Cox analysis of clinicopathological factors and risk signatures.", "rows": [["Variable", "Univariate Cox analysis of clinicopathologicalfactors and risk signatures", "Multivariate Cox analysis of clinicopathologicalfactors and risk signatures"], ["TCGA-train dataset"], ["id", "HR", "95% CI", "p-value", "HR", "95% CI", "p-value"], ["age", "1.02", "1.00–1.04", "0.013", "1.01", "0.99–1.03", "0.221"], ["gender", "1.11", "0.73–1.49", "0.621", "1.25", "0.79–1.71", "0.339"], ["stage", "1.54", "1.20–1.88", "0.001", "1.56", "1.20–1.92", "0.001"], ["riskScore", "10.41", "6.43–14.39", "1.49E-21", "10.64", "6.47–14.81", "1.15E-20"], ["TCGA-test dataset"], ["id", "HR", "95% CI", "p-value", "HR", "95% CI", "p-value"], ["age", "1.02", "1.01–1.03", "0.002", "1.02", "1.01–1.03", "0.002"], ["gender", "0.94", "0.60–1.28", "0.805", "0.84", "0.53–1.15", "0.469"], ["stage", "1.27", "1.02–1.52", "0.036", "1.3", "1.03–1.57", "0.029"], ["riskScore", "2.12", "1.44–2.80", "0", "2.08", "1.41–2.75", "0.0002"], ["TCGA dataset"], ["id", "HR", "95% CI", "p-value", "HR", "95% CI", "p-value"], ["age", "1.02", "1.01–1.03", "0.011", "1.01", "0.98–1.04", "0.010"], ["gender", "1.04", "0.60–1.48", "0.701", "1.02", "0.61–1.43", "0.412"], ["stage", "1.42", "1.31–1.63", "0.006", "1.13", "0.83–1.43", "0.008"], ["riskScore", "6.32", "2.14–10.50", "0.002", "5.11", "3.12–7.10", "0.009"], ["GSE65904 validation dataset"], ["id", "HR", "95% CI", "p-value", "HR", "95% CI", "p-value"], ["age", "0.99", "0.98–1.01", "0.567", "1", "0.99–1.02", "0.592"], ["gender", "1.37", "0.90–1.84", "0.143", "1.31", "0.86–1.76", "0.205"], ["stage", "2.35", "1.53–3.17", "8.55E-05", "2.77", "1.78–3.76", "5.53E-06"], ["riskScore", "1.76", "1.34–2.18", "4.48E-05", "1.98", "1.49–2.47", "1.87E-06"], ["GSE59455 validation dataset"], ["id", "HR", "95% CI", "p-value", "HR", "95% CI", "p-value"], ["age", "0.99", "0.98–1.00", "0.177", "0.99", "0.98–1.00", "0.112"], ["gender", "1.24", "0.84–1.64", "0.283", "1.17", "0.80–1.54", "0.421"], ["stage", "0.77", "0.67–0.87", "0", "0.76", "0.66–0.86", "8.68E-05"], ["riskScore", "1.35", "0.78–1.92", "0.141", "1.64", "0.94–2.34", "0.042"], ["GSE22153 validation dataset"], ["id", "HR", "95% CI", "p-value", "HR", "95% CI", "p-value"], ["age", "1.01", "0.99–1.03", "0.372", "1.01", "0.99–1.03", "0.547"], ["gender", "0.99", "0.55–1.43", "0.967", "1.32", "0.71–1.93", "0.378"], ["stage", "1.69", "0.66–2.72", "0.27", "1.05", "0.33–1.77", "0.938"], ["riskScore", "1.95", "1.15–2.75", "0.013", "2.07", "1.16–2.98", "0.014"]], "row_count": 37, "column_count": 7, "numeric_cells": 159, "header_rows": 1, "locator": "section[11]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE22153 not downloaded", "asset:data:geo:GSE22153 licence not read", "asset:data:geo:GSE59455 not downloaded", "asset:data:geo:GSE59455 licence not read", "asset:data:geo:GSE65904 not downloaded", "asset:data:geo:GSE65904 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Based on the results of a log-rank test, IRGPs with a false discovery rate (FDR) <0.001 (n = 23) were retained and entered into a least absolute shrinkage and selection operator (LASSO) penalized Cox regression model (iterations = 1000)."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}], "targets": [], "gaps": []}, "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE65904", "GSE59455", "GSE22153"], "resolved_accessions": ["GSE65904", "GSE59455", "GSE22153"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: TCGA dataset (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga); GEO dataset (https://www.ncbi.nlm.nih.gov/gds/): GSE65904, GSE59455, and GSE22153."], "basis": "The paper names GSE65904, GSE59455, GSE22153 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:33193373", "data:geo:GSE22153", "asset:table:pmid:33193373:1", "asset:table:pmid:33193373:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22153"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 50112, "completion_tokens": 2848, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33193373", "type": "paper", "label": "pmid:33193373"}, {"id": "source:pmid:33193373", "type": "manuscript", "label": "PMID 33193373 full text"}, {"id": "data:geo:GSE22153", "type": "dataset", "label": "GEO GSE22153"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33193373", "type": "paper", "label": "pmid:33193373"}, {"id": "source:pmid:33193373", "type": "manuscript", "label": "PMID 33193373 full text"}, {"id": "data:geo:GSE22153", "type": "dataset", "label": "GEO GSE22153"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33193373", "type": "extraction", "used": ["source:pmid:33193373"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22153", "type": "accession_resolution", "used": ["data:geo:GSE22153"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33193373", "parent_hash": "sha256:472375ababc82a1399f7c8d7e2db2db4e79d1f863b5cce21b8a1bcd38e3b3d6b", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE22153 licence not read", "asset:data:geo:GSE22153 not downloaded", "asset:data:geo:GSE59455 licence not read", "asset:data:geo:GSE59455 not downloaded", "asset:data:geo:GSE65904 licence not read", "asset:data:geo:GSE65904 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["n this retrospective study, four independent RNA-seq datasets and clinical data from diverse, hig"], "order_basis": "paper_text_order:1080", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ll population based on gene expression data. Immunohistochemical images of CM patients were downloaded from T", "gure 8G ). These results correlated with the immunohistochemical results downloaded from The Human Protein At", "ficant expressed in high risk group (G). (H) IHC result of PD-1 protein in high risk group. S", "egative; quantity, none; location, none. (I) IHC result of PD-1 protein in low risk group. St"], "order_basis": "paper_text_order:1942", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Based on the results of a log-rank test, IRGPs with a false discovery rate (FDR) <0.001 (n = 23) were retained and entered into a least absolute shrinkage and selection operator (LASSO) penalized Cox regression model (iterations = 1000)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}