← All .science files
pmid:34413861
Comprehensive Characterization of RNA Processing Factors in Gastric Cancer Identifies a Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses.
Shenghan Lou · Fanzheng Meng · Xin Yin · Yao Zhang · Bangling Han · Yingwei Xue
Frontiers in immunology · 2021 doi:10.3389/fimmu.2021.719628
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 · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] 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 · 10 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 200 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 300 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 5 items
[1] array · 2 items
[2] array · 6 items
[3] array · 5 items
[4] array · 5 items
[5] array · 6 items
[6] array · 5 items
[7] array · 5 items
[8] array · 6 items
[9] array · 5 items
[10] array · 5 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 14 items
[0] array · 4 items
[1] array · 4 items
[2] array · 6 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 6 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 6 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 29 items
[0] array · 4 items
[1] array · 3 items
[2] array · 6 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 6 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 6 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 5 items
[1] array · 2 items
[2] array · 6 items
[3] array · 5 items
[4] array · 5 items
[5] array · 6 items
[6] array · 5 items
[7] array · 5 items
[8] array · 6 items
[9] array · 5 items
[10] array · 5 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 14 items
[0] array · 4 items
[1] array · 4 items
[2] array · 6 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 6 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 6 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[9] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 29 items
[0] array · 4 items
[1] array · 3 items
[2] array · 6 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 6 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 6 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 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
evidence object · 3 fields
[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 · 1 item
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 · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 8 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 · 1 item
[0] 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:34413861", "kind": "science-record", "revision": 6, "content_hash": "sha256:229d3aefe290da62988d27089318112af1784aafeee8e1acdb7301ac53a2cb14", "created_at": "2026-11-01T15:41:48Z", "updated_at": "2026-11-01T21:26:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Characterization of RNA Processing Factors in Gastric Cancer Identifies a Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses.", "doi": "10.3389/fimmu.2021.719628", "pmid": "34413861", "authors": ["Shenghan Lou", "Fanzheng Meng", "Xin Yin", "Yao Zhang", "Bangling Han", "Yingwei Xue"], "journal": "Frontiers in immunology", "year": 2021, "abstract": "RNA processing converts primary transcript RNA into mature RNA. Altered RNA processing drives tumor initiation and maintenance, and may generate novel therapeutic opportunities. However, the role of RNA processing factors in gastric cancer (GC) has not been clearly elucidated. This study presents a comprehensive analysis exploring the clinical, molecular, immune, and drug response features underlying the RNA processing factors in GC. This study included 1079 GC cases from The Cancer Genome Atlas (TCGA, training set), our hospital cohort, and two other external validation sets (GSE15459, GSE62254). We developed an RNA processing-related prognostic signature using Cox regression with the least absolute shrinkage and selection operator (LASSO) penalty. The prognostic value of the signature was evaluated using a multiple-method approach. The genetic variants, pathway activation, immune heterogeneity, drug response, and splicing features associated with the risk signature were explored using bioinformatics methods. Among the tested 819 RNA processing genes, we identified five distinct RNA processing patterns with specific clinical outcomes and biological features. A 10-gene RNA processing-related prognostic signature, involving ZBTB7A, METTL2B, CACTIN, TRUB2, POLDIP3, TSEN54, SUGP1, RBMS1, TGFB1, and PWP2, was further identified. The signature was a powerful and robust prognosis factor in both the training and validation datasets. Notably, it could stratify the survival of patients with GC in specific tumor-node-metastasis (TNM) classification subgroups. We constructed a composite prognostic nomogram to facilitate clinical practice by integrating this signature with other clinical variables (TNM stage, age). Patients with low-risk scores were characterized with good clinical outcomes, proliferation, and metabolism hallmarks. Conversely, poor clinical outcome, invasion, and metastasis hallmarks were enriched in the high-risk group. The RNA processing signature was also involved in tumor microenvironment reprogramming and regulating alternative splicing, causing different drug response features between the two risk groups. The low-risk subgroup was characterized by high genomic instability, high alternative splicing and might benefit from the immunotherapy. Our findings highlight the prognostic value of RNA processing factors for patients with GC and provide insights into the specific clinical and molecular features underlying the RNA processing-related signature, which may be important for patient management and targeting treatment.", "claims": [{"id": "claim-method", "statement": "Univariate Cox proportional hazards regression analysis was first performed on the expression matrix of RNA processing factors to estimate the relationship between RNA processing factors and prognosis (OS) in the TCGA-STAD cohort. RNA processing factors with p-value < 0.1 were selected as the potential prognosis-related RNA processing factors. The least absolute shrinkage and selection operator (LASSO) penalty was performed in the discovery cohort to build an optimal prognostic signature with the minimum number of RNA processing factors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34413861", "locator": "sections[7] \"Identification of the RNA Processing-Related Prognostic Signature\" paragraph 2", "quote": "Univariate Cox proportional hazards regression analysis was first performed on the expression matrix of RNA processing factors to estimate the relationship between RNA processing factors and prognosis (OS) in the TCGA-STAD cohort."}, {"asset": "source:pmid:34413861", "locator": "sections[7] \"Identification of the RNA Processing-Related Prognostic Signature\" paragraph 2", "quote": "RNA processing factors with p-value < 0.1 were selected as the potential prognosis-related RNA processing factors."}, {"asset": "source:pmid:34413861", "locator": "sections[7] \"Identification of the RNA Processing-Related Prognostic Signature\" paragraph 3", "quote": "The least absolute shrinkage and selection operator (LASSO) penalty was performed in the discovery cohort to build an optimal prognostic signature with the minimum number of RNA processing factors."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34413861", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "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:34413861"], "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:GSE15459"], "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:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34413861", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2021.719628", "sha256": "sha256:48fb52eb40e43720adb026095ef03ecbb740e059730ed992265945169f30d866", "bytes": 60333, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2021.719628", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8369824", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15459", "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=GSE15459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15459", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM387788", "GSM387789", "GSM387790", "GSM387791", "GSM387792", "GSM387793", "GSM387794", "GSM387795", "GSM387796", "GSM387797", "GSM387798", "GSM387799", "GSM387800", "GSM387801", "GSM387802", "GSM387803", "GSM387804", "GSM387805", "GSM387806", "GSM387807", "GSM387808", "GSM387809", "GSM387810", "GSM387811", "GSM387812", "GSM387813", "GSM387814", "GSM387815", "GSM387816", "GSM387817", "GSM387818", "GSM387819", "GSM387820", "GSM387821", "GSM387822", "GSM387823", "GSM387824", "GSM387825", "GSM387826", "GSM387827", "GSM387828", "GSM387829", "GSM387830", "GSM387831", "GSM387832", "GSM387833", "GSM387834", "GSM387835", "GSM387836", "GSM387837", "GSM387838", "GSM387839", "GSM387840", "GSM387841", "GSM387842", "GSM387843", "GSM387844", "GSM387845", "GSM387846", "GSM387847", "GSM387848", "GSM387849", "GSM387850", "GSM387851", "GSM387852", "GSM387853", "GSM387854", "GSM387855", "GSM387856", "GSM387857", "GSM387858", "GSM387859", "GSM387860", "GSM387861", "GSM387862", "GSM387863", "GSM387864", "GSM387865", "GSM387866", "GSM387867", "GSM387868", "GSM387869", "GSM387870", "GSM387871", "GSM387872", "GSM387873", "GSM387874", "GSM387875", "GSM387876", "GSM387877", "GSM387878", "GSM387879", "GSM387880", "GSM387881", "GSM387882", "GSM387883", "GSM387884", "GSM387885", "GSM387886", "GSM387887", "GSM387888", "GSM387889", "GSM387890", "GSM387891", "GSM387892", "GSM387893", "GSM387894", "GSM387895", "GSM387896", "GSM387897", "GSM387898", "GSM387899", "GSM387900", "GSM387901", "GSM387902", "GSM387903", "GSM387904", "GSM387905", "GSM387906", "GSM387907", "GSM387908", "GSM387909", "GSM387910", "GSM387911", "GSM387912", "GSM387913", "GSM387914", "GSM387915", "GSM387916", "GSM387917", "GSM387918", "GSM387919", "GSM387920", "GSM387921", "GSM387922", "GSM387923", "GSM387924", "GSM387925", "GSM387926", "GSM387927", "GSM387928", "GSM387929", "GSM387930", "GSM387931", "GSM387932", "GSM387933", "GSM387934", "GSM387935", "GSM387936", "GSM387937", "GSM387938", "GSM387939", "GSM387940", "GSM387941", "GSM387942", "GSM387943", "GSM387944", "GSM387945", "GSM387946", "GSM387947", "GSM387948", "GSM387949", "GSM387950", "GSM387951", "GSM387952", "GSM387953", "GSM387954", "GSM387955", "GSM387956", "GSM387957", "GSM387958", "GSM387959", "GSM387960", "GSM387961", "GSM387962", "GSM387963", "GSM387964", "GSM387965", "GSM387966", "GSM387967", "GSM387968", "GSM387969", "GSM387970", "GSM387971", "GSM387972", "GSM387973", "GSM387974", "GSM387975", "GSM387976", "GSM387977", "GSM387978", "GSM387979", "GSM387980", "GSM387981", "GSM387982", "GSM387983", "GSM387984", "GSM387985", "GSM387986", "GSM387987"], "sample_count": 200, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gastric Cancer Project '08 (Singapore Patient Cohort)", "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:GSE62254", "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=GSE62254", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62254", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1523727", "GSM1523728", "GSM1523729", "GSM1523744", "GSM1523745", "GSM1523746", "GSM1523747", "GSM1523748", "GSM1523765", "GSM1523768", "GSM1523769", "GSM1523770", "GSM1523771", "GSM1523772", "GSM1523773", "GSM1523774", "GSM1523775", "GSM1523776", "GSM1523777", "GSM1523778", "GSM1523779", "GSM1523780", "GSM1523781", "GSM1523782", "GSM1523783", "GSM1523784", "GSM1523785", "GSM1523786", "GSM1523787", "GSM1523788", "GSM1523789", "GSM1523790", "GSM1523791", "GSM1523792", "GSM1523793", "GSM1523794", "GSM1523795", "GSM1523796", "GSM1523797", "GSM1523798", "GSM1523799", "GSM1523800", "GSM1523801", "GSM1523802", "GSM1523803", "GSM1523804", "GSM1523805", "GSM1523806", "GSM1523807", "GSM1523808", "GSM1523809", "GSM1523810", "GSM1523811", "GSM1523812", "GSM1523813", "GSM1523814", "GSM1523815", "GSM1523816", "GSM1523817", "GSM1523818", "GSM1523819", "GSM1523820", "GSM1523821", "GSM1523822", "GSM1523823", "GSM1523824", "GSM1523825", "GSM1523826", "GSM1523827", "GSM1523828", "GSM1523829", "GSM1523830", "GSM1523831", "GSM1523832", "GSM1523833", "GSM1523834", "GSM1523835", "GSM1523836", "GSM1523837", "GSM1523838", "GSM1523839", "GSM1523840", "GSM1523841", "GSM1523842", "GSM1523843", "GSM1523844", "GSM1523845", "GSM1523846", "GSM1523847", "GSM1523848", "GSM1523849", "GSM1523850", "GSM1523851", "GSM1523852", "GSM1523853", "GSM1523854", "GSM1523855", "GSM1523856", "GSM1523857", "GSM1523858", "GSM1523859", "GSM1523860", "GSM1523861", "GSM1523862", "GSM1523863", "GSM1523864", "GSM1523865", "GSM1523866", "GSM1523867", "GSM1523868", "GSM1523869", "GSM1523870", "GSM1523871", "GSM1523872", "GSM1523873", "GSM1523874", "GSM1523875", "GSM1523876", "GSM1523877", "GSM1523878", "GSM1523879", "GSM1523880", "GSM1523881", "GSM1523882", "GSM1523883", "GSM1523884", "GSM1523885", "GSM1523886", "GSM1523887", "GSM1523888", "GSM1523889", "GSM1523890", "GSM1523891", "GSM1523892", "GSM1523893", "GSM1523894", "GSM1523895", "GSM1523896", "GSM1523897", "GSM1523898", "GSM1523899", "GSM1523901", "GSM1523903", "GSM1523904", "GSM1523905", "GSM1523906", "GSM1523908", "GSM1523909", "GSM1523910", "GSM1523911", "GSM1523918", "GSM1523919", "GSM1523920", "GSM1523921", "GSM1523922", "GSM1523923", "GSM1523924", "GSM1523925", "GSM1523926", "GSM1523927", "GSM1523928", "GSM1523929", "GSM1523930", "GSM1523931", "GSM1523932", "GSM1523933", "GSM1523934", "GSM1523935", "GSM1523936", "GSM1523937", "GSM1523938", "GSM1523939", "GSM1523940", "GSM1523941", "GSM1523942", "GSM1523943", "GSM1523944", "GSM1523945", "GSM1523946", "GSM1523947", "GSM1523948", "GSM1523949", "GSM1523950", "GSM1523951", "GSM1523952", "GSM1523953", "GSM1523954", "GSM1523955", "GSM1523956", "GSM1523957", "GSM1523958", "GSM1523959", "GSM1523960", "GSM1523961", "GSM1523962", "GSM1523963", "GSM1523964", "GSM1523965", "GSM1523966", "GSM1523967", "GSM1523968", "GSM1523969", "GSM1523970", "GSM1523971", "GSM1523972", "GSM1523973", "GSM1523974", "GSM1523975", "GSM1523976", "GSM1523977", "GSM1523978", "GSM1523979", "GSM1523980", "GSM1523981", "GSM1523982", "GSM1523983", "GSM1523984", "GSM1523985", "GSM1523986", "GSM1523987", "GSM1523988", "GSM1523989", "GSM1523990", "GSM1523991", "GSM1523992", "GSM1523993", "GSM1523994", "GSM1523995", "GSM1523996", "GSM1523997", "GSM1523998", "GSM1523999", "GSM1524000", "GSM1524001", "GSM1524002", "GSM1524003", "GSM1524004", "GSM1524005", "GSM1524006", "GSM1524007", "GSM1524008", "GSM1524009", "GSM1524010", "GSM1524011", "GSM1524012", "GSM1524013", "GSM1524014", "GSM1524015", "GSM1524016", "GSM1524017", "GSM1524018", "GSM1524019", "GSM1524020", "GSM1524021", "GSM1524022", "GSM1524023", "GSM1524024", "GSM1524025", "GSM1524026", "GSM1524027", "GSM1524028", "GSM1524029", "GSM1524030", "GSM1524031", "GSM1524032", "GSM1524033", "GSM1524034", "GSM1524035", "GSM1524036", "GSM1524037", "GSM1524038", "GSM1524039", "GSM1524040", "GSM1524041", "GSM1524042", "GSM1524043", "GSM1524044", "GSM1524045", "GSM1524046", "GSM1524047", "GSM1524048", "GSM1524049", "GSM1524050", "GSM1524051", "GSM1524052", "GSM1524053", "GSM1524054", "GSM1524055", "GSM1524056", "GSM1524057", "GSM1524058", "GSM1524059", "GSM1524060", "GSM1524061", "GSM1524062", "GSM1524068", "GSM1524069", "GSM1524070", "GSM1524071", "GSM1524072"], "sample_count": 300, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors]", "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:PRJNA718168", "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=PRJNA718168", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA718168", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:56Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34413861:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2ef6ebbff0063ba2fe323c92d6303a208c31690543710bcbec77f4c461e96dbc", "bytes": 1273, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T1", "version": null, "note": "RMS time (RMST) between the two risk groups at different time points.", "structure": {"pmcid": "PMC8369824", "section_index": 7, "section_title": "Identification of the RNA Processing-Related Prognostic Signature", "row_count": 11, "column_count": 6}, "table": {"label": "Table 1", "caption": "RMS time (RMST) between the two risk groups at different time points.", "rows": [["Dataset", "Time point", "RMSTa", "RMST differenceb", "p-value"], ["Low risk (95% CI)", "High risk (95% CI)"], ["TCGA cohort (n = 373)", "12 months", "11.236 (10.881, 11.590)", "10.206 (9.722, 10.69)", "1.030 (0.430, 1.629)", "<0.001"], ["36 months", "28.138 (26.304, 29.972)", "21.273 (19.167, 23.378)", "6.865 (4.073, 9.658)", "<0.001"], ["60 months", "40.810 (36.656, 44.964)", "29.399 (25.410, 33.387)", "11.411 (5.652, 17.170)", "<0.001"], ["HMU cohort (n = 214)", "12 months", "11.046 (10.594, 11.498)", "11.072 (10.700, 11.444)", "-0.026 (-0.612, 0.559)", "0.93"], ["36 months", "29.787 (27.582, 31.992)", "25.915 (23.592, 28.237)", "3.872 (0.670, 7.075)", "0.018"], ["60 months", "43.591 (39.832, 47.350)", "34.980 (30.935, 39.025)", "8.611 (3.089, 14.133)", "0.002"], ["GEO cohort (n = 492)", "12 months", "11.242 (10.965, 11.519)", "11.115 (10.852, 11.377)", "0.127 (-0.255, 0.509)", "0.514"], ["36 months", "28.479 (27.011, 29.948)", "25.578 (24.070, 27.085)", "2.901 (0.797, 5.006)", "0.007"], ["60 months", "42.934 (40.076, 45.792)", "36.224 (33.359, 39.089)", "6.710 (2.663, 10.757)", "0.001"]], "row_count": 11, "column_count": 6, "numeric_cells": 50, "header_rows": 2, "locator": "section[16]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34413861:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3fc01a961e08156eb950b23313d21ee69fce52770cdda615a474f3ae99b16ef5", "bytes": 1374, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T2", "version": null, "note": "Univariate and multivariate Cox analyses of the RNA processing-related signature.", "structure": {"pmcid": "PMC8369824", "section_index": 7, "section_title": "Identification of the RNA Processing-Related Prognostic Signature", "row_count": 14, "column_count": 6}, "table": {"label": "Table 2", "caption": "Univariate and multivariate Cox analyses of the RNA processing-related signature.", "rows": [["Dataset", "Factor", "Univariate", "Multivariate"], ["HR (95% CI)", "p-value", "HR (95% CI)", "p-value"], ["TCGA cohort (n = 373)", "Risk score (increasing values)", "9.280 (4.746, 18.148)", "<0.001", "9.918 (4.926, 19.968)", "<0.001"], ["Age (increasing years)", "1.021 (1.005, 1.037)", "0.012", "1.027 (1.010, 1.045)", "0.002"], ["Sex (male vs. female)", "1.333 (0.936, 1.899)", "0.112", "", ""], ["TNM stage (III + IV vs. I + II)", "1.891 (1.325, 2.698)", "<0.001", "2.101 (1.464, 3.015)", "<0.001"], ["HMU cohort (n = 214)", "Risk score (increasing values)", "2.819 (1.041, 7.637)", "0.041", "2.819 (1.041, 7.637)", "0.041"], ["Age (increasing years)", "1.009 (0.992, 1.027)", "0.284", "", ""], ["Sex (male vs. female)", "0.984 (0.615, 1.574)", "0.947", "", ""], ["TNM stage (III + IV vs. I + II)", "1.165 (0.710, 1.911)", "0.545", "", ""], ["GEO cohort (n = 492)", "Risk score (increasing values)", "3.601 (2.002, 6.474)", "<0.001", "1.632 (0.879, 3.029)", "0.121"], ["Age (increasing years)", "1.006 (0.995, 1.018)", "0.254", "", ""], ["Sex (male vs. female)", "1.056 (0.810, 1.377)", "0.686", "", ""], ["TNM stage (III + IV vs. I + II)", "4.245 (3.097, 5.817)", "<0.001", "3.983 (2.878, 5.511)", "<0.001"]], "row_count": 14, "column_count": 6, "numeric_cells": 41, "header_rows": 2, "locator": "section[16]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34413861:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b624286a69f5767855386635004d806a1601c48cdcabb6e77395833a3784883a", "bytes": 1681, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[3]#T3", "version": null, "note": "Subgroup analysis of the RNA processing-related signature.", "structure": {"pmcid": "PMC8369824", "section_index": 7, "section_title": "Identification of the RNA Processing-Related Prognostic Signature", "row_count": 29, "column_count": 6}, "table": {"label": "Table 3", "caption": "Subgroup analysis of the RNA processing-related signature.", "rows": [["Data set", "Factor", "Subgroup analysis", "p-value for interaction"], ["Samples", "HR (95% CI)", "p-value"], ["TCGA cohort (n = 373)", "Sex", "", "", "", ""], ["Female", "133.000", "12.071 (3.737, 38.996)", "<0.001", "0.651"], ["Male", "240.000", "8.271 (3.611, 18.945)", "<0.001", ""], ["Age", "", "", "", ""], ["≤60", "120.000", "18.021 (4.949, 65.616)", "<0.001", "0.268"], ["> 60", "249.000", "7.543 (3.498, 16.267)", "<0.001", ""], ["Stage", "", "", "", ""], ["Early (I and II)", "164.000", "7.482 (2.349, 23.831)", "0.001", "0.660"], ["Advanced (III and IV)", "186.000", "11.097 (4.527, 27.202)", "<0.001", ""], ["HMU cohort (n = 214)", "Sex", "", "", "", ""], ["Female", "77.000", "2.162 (0.315, 14.849)", "0.433", "0.666"], ["Male", "136.000", "3.372 (1.037, 10.971)", "0.043", ""], ["Age", "", "", "", ""], ["≤60", "118.000", "2.369 (0.563, 9.977)", "0.240", "0.691"], ["> 60", "96.000", "3.509 (0.883, 13.943)", "0.075", ""], ["Stage", "", "", "", ""], ["Early (I and II)", "67.000", "1.243 (0.213, 7.264)", "0.809", "0.260"], ["Advanced (III and IV)", "147.000", "4.149 (1.234, 13.947)", "0.021", ""], ["GEO cohort (n = 492)", "Sex", "", "", "", ""], ["Female", "168.000", "6.633 (2.354, 18.691)", "<0.001", "0.113"], ["Male", "324.000", "2.651 (1.290, 5.447)", "0.008", ""], ["Age", "", "", "", ""], ["≤60", "178.000", "8.792 (3.039, 25.438)", "<0.001", "0.065"], ["> 60", "314.000", "2.583 (1.260, 5.291)", "0.010", ""], ["Stage", "", "", "", ""], ["Early (I and II)", "187.000", "2.796 (0.784, 9.976)", "0.113", "0.312"], ["Advanced (III and IV)", "305.000", "1.331 (0.654, 2.708)", "0.431", ""]], "row_count": 29, "column_count": 6, "numeric_cells": 73, "header_rows": 2, "locator": "section[16]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:34413861:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2ef6ebbff0063ba2fe323c92d6303a208c31690543710bcbec77f4c461e96dbc", "bytes": 1273, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T1", "version": null, "note": "RMS time (RMST) between the two risk groups at different time points.", "structure": {"pmcid": "PMC8369824", "section_index": 16, "section_title": "Identification of the RNA Processing-Related Prognostic Signature", "row_count": 11, "column_count": 6}, "table": {"label": "Table 1", "caption": "RMS time (RMST) between the two risk groups at different time points.", "rows": [["Dataset", "Time point", "RMSTa", "RMST differenceb", "p-value"], ["Low risk (95% CI)", "High risk (95% CI)"], ["TCGA cohort (n = 373)", "12 months", "11.236 (10.881, 11.590)", "10.206 (9.722, 10.69)", "1.030 (0.430, 1.629)", "<0.001"], ["36 months", "28.138 (26.304, 29.972)", "21.273 (19.167, 23.378)", "6.865 (4.073, 9.658)", "<0.001"], ["60 months", "40.810 (36.656, 44.964)", "29.399 (25.410, 33.387)", "11.411 (5.652, 17.170)", "<0.001"], ["HMU cohort (n = 214)", "12 months", "11.046 (10.594, 11.498)", "11.072 (10.700, 11.444)", "-0.026 (-0.612, 0.559)", "0.93"], ["36 months", "29.787 (27.582, 31.992)", "25.915 (23.592, 28.237)", "3.872 (0.670, 7.075)", "0.018"], ["60 months", "43.591 (39.832, 47.350)", "34.980 (30.935, 39.025)", "8.611 (3.089, 14.133)", "0.002"], ["GEO cohort (n = 492)", "12 months", "11.242 (10.965, 11.519)", "11.115 (10.852, 11.377)", "0.127 (-0.255, 0.509)", "0.514"], ["36 months", "28.479 (27.011, 29.948)", "25.578 (24.070, 27.085)", "2.901 (0.797, 5.006)", "0.007"], ["60 months", "42.934 (40.076, 45.792)", "36.224 (33.359, 39.089)", "6.710 (2.663, 10.757)", "0.001"]], "row_count": 11, "column_count": 6, "numeric_cells": 50, "header_rows": 2, "locator": "section[16]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34413861:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3fc01a961e08156eb950b23313d21ee69fce52770cdda615a474f3ae99b16ef5", "bytes": 1374, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T2", "version": null, "note": "Univariate and multivariate Cox analyses of the RNA processing-related signature.", "structure": {"pmcid": "PMC8369824", "section_index": 16, "section_title": "Identification of the RNA Processing-Related Prognostic Signature", "row_count": 14, "column_count": 6}, "table": {"label": "Table 2", "caption": "Univariate and multivariate Cox analyses of the RNA processing-related signature.", "rows": [["Dataset", "Factor", "Univariate", "Multivariate"], ["HR (95% CI)", "p-value", "HR (95% CI)", "p-value"], ["TCGA cohort (n = 373)", "Risk score (increasing values)", "9.280 (4.746, 18.148)", "<0.001", "9.918 (4.926, 19.968)", "<0.001"], ["Age (increasing years)", "1.021 (1.005, 1.037)", "0.012", "1.027 (1.010, 1.045)", "0.002"], ["Sex (male vs. female)", "1.333 (0.936, 1.899)", "0.112", "", ""], ["TNM stage (III + IV vs. I + II)", "1.891 (1.325, 2.698)", "<0.001", "2.101 (1.464, 3.015)", "<0.001"], ["HMU cohort (n = 214)", "Risk score (increasing values)", "2.819 (1.041, 7.637)", "0.041", "2.819 (1.041, 7.637)", "0.041"], ["Age (increasing years)", "1.009 (0.992, 1.027)", "0.284", "", ""], ["Sex (male vs. female)", "0.984 (0.615, 1.574)", "0.947", "", ""], ["TNM stage (III + IV vs. I + II)", "1.165 (0.710, 1.911)", "0.545", "", ""], ["GEO cohort (n = 492)", "Risk score (increasing values)", "3.601 (2.002, 6.474)", "<0.001", "1.632 (0.879, 3.029)", "0.121"], ["Age (increasing years)", "1.006 (0.995, 1.018)", "0.254", "", ""], ["Sex (male vs. female)", "1.056 (0.810, 1.377)", "0.686", "", ""], ["TNM stage (III + IV vs. I + II)", "4.245 (3.097, 5.817)", "<0.001", "3.983 (2.878, 5.511)", "<0.001"]], "row_count": 14, "column_count": 6, "numeric_cells": 41, "header_rows": 2, "locator": "section[16]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34413861:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b624286a69f5767855386635004d806a1601c48cdcabb6e77395833a3784883a", "bytes": 1681, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[3]#T3", "version": null, "note": "Subgroup analysis of the RNA processing-related signature.", "structure": {"pmcid": "PMC8369824", "section_index": 16, "section_title": "Identification of the RNA Processing-Related Prognostic Signature", "row_count": 29, "column_count": 6}, "table": {"label": "Table 3", "caption": "Subgroup analysis of the RNA processing-related signature.", "rows": [["Data set", "Factor", "Subgroup analysis", "p-value for interaction"], ["Samples", "HR (95% CI)", "p-value"], ["TCGA cohort (n = 373)", "Sex", "", "", "", ""], ["Female", "133.000", "12.071 (3.737, 38.996)", "<0.001", "0.651"], ["Male", "240.000", "8.271 (3.611, 18.945)", "<0.001", ""], ["Age", "", "", "", ""], ["≤60", "120.000", "18.021 (4.949, 65.616)", "<0.001", "0.268"], ["> 60", "249.000", "7.543 (3.498, 16.267)", "<0.001", ""], ["Stage", "", "", "", ""], ["Early (I and II)", "164.000", "7.482 (2.349, 23.831)", "0.001", "0.660"], ["Advanced (III and IV)", "186.000", "11.097 (4.527, 27.202)", "<0.001", ""], ["HMU cohort (n = 214)", "Sex", "", "", "", ""], ["Female", "77.000", "2.162 (0.315, 14.849)", "0.433", "0.666"], ["Male", "136.000", "3.372 (1.037, 10.971)", "0.043", ""], ["Age", "", "", "", ""], ["≤60", "118.000", "2.369 (0.563, 9.977)", "0.240", "0.691"], ["> 60", "96.000", "3.509 (0.883, 13.943)", "0.075", ""], ["Stage", "", "", "", ""], ["Early (I and II)", "67.000", "1.243 (0.213, 7.264)", "0.809", "0.260"], ["Advanced (III and IV)", "147.000", "4.149 (1.234, 13.947)", "0.021", ""], ["GEO cohort (n = 492)", "Sex", "", "", "", ""], ["Female", "168.000", "6.633 (2.354, 18.691)", "<0.001", "0.113"], ["Male", "324.000", "2.651 (1.290, 5.447)", "0.008", ""], ["Age", "", "", "", ""], ["≤60", "178.000", "8.792 (3.039, 25.438)", "<0.001", "0.065"], ["> 60", "314.000", "2.583 (1.260, 5.291)", "0.010", ""], ["Stage", "", "", "", ""], ["Early (I and II)", "187.000", "2.796 (0.784, 9.976)", "0.113", "0.312"], ["Advanced (III and IV)", "305.000", "1.331 (0.654, 2.708)", "0.431", ""]], "row_count": 29, "column_count": 6, "numeric_cells": 73, "header_rows": 2, "locator": "section[16]/table-wrap[3]#T3"}}], "gaps": ["asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:PRJNA718168 not downloaded", "asset:data:geo:PRJNA718168 licence not read"]}, "analysis": {"state": "complete", "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": "reordered", "quote": "Univariate Cox proportional hazards regression analysis was first performed on the expression matrix of RNA processing factors to estimate the relationship between RNA processing factors and prognosis (OS) in the TCGA-STAD cohort. RNA processing factors with p-value < 0.1 were selected as the potential prognosis-related RNA processing factors. The least absolute shrinkage and selection operator (LASSO) penalty was performed in the discovery cohort to build an optimal prognostic signature with the minimum number of RNA processing factors."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-3", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}], "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": ["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": ["PRJNA718168", "GSE15459", "GSE62254"], "resolved_accessions": ["GSE15459", "GSE62254"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE15459, GSE62254 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": ["cox_ph"], "assets": ["source:pmid:34413861", "data:geo:GSE15459", "asset:table:pmid:34413861:1", "asset:table:pmid:34413861:2", "asset:table:pmid:34413861:3", "asset:table:pmid:34413861:4", "asset:table:pmid:34413861:5", "asset:table:pmid:34413861:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15459"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:49Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 38537, "completion_tokens": 3261, "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:34413861", "type": "paper", "label": "pmid:34413861"}, {"id": "source:pmid:34413861", "type": "manuscript", "label": "PMID 34413861 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34413861", "type": "paper", "label": "pmid:34413861"}, {"id": "source:pmid:34413861", "type": "manuscript", "label": "PMID 34413861 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34413861", "type": "extraction", "used": ["source:pmid:34413861"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15459", "type": "accession_resolution", "used": ["data:geo:GSE15459"], "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:34413861", "parent_hash": "sha256:5ed011af9dd44cbfb9ef80d644ba1e82a96ae5f2b78ec39adbe1f9f34166d161", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:PRJNA718168 licence not read", "asset:data:geo:PRJNA718168 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate Cox proportional hazards regression analysis was first performed on the expression matrix of RNA processing factors to estimate the relationship between RNA processing factors and prognosis (OS) in the TCGA-STAD cohort. RNA processing factors with p-value < 0.1 were selected as the potential prognosis-related RNA processing factors. The least absolute shrinkage and selection operator (LASSO) penalty was performed in the discovery cohort to build an optimal prognostic signature with the minimum number of RNA processing factors."], "order_basis": "analysis_only", "id": "assay:1"}]}