← All .science files
pmid:34590792
SEC61G overexpression and DNA amplification correlates with prognosis and immune cell infiltration in head and neck squamous cell carcinoma.
Tianzhu Lu · Yiping Chen · Xiaochang Gong · Qiaojuan Guo · Canyang Lin · Qingfeng Luo · Ziwei Tu · Jianji Pan · Jingao Li
Cancer medicine · 2021 doi:10.1002/cam4.4301
Paper
complete
Experiment
partial
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 · 9 items
claims array · 1 item
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 · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
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 · 1 item
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 30 items
[0] array · 3 items
[1] array · 2 items
[2] array · 1 item
[3] array · 3 items
[4] array · 3 items
[5] array · 1 item
[6] array · 3 items
[7] array · 3 items
[8] array · 1 item
[9] array · 3 items
[10] array · 3 items
[11] array · 1 item
[12] array · 3 items
[13] array · 3 items
[14] array · 3 items
[15] array · 3 items
[16] array · 1 item
[17] array · 3 items
[18] array · 3 items
[19] array · 3 items
[20] array · 3 items
[21] array · 1 item
[22] array · 3 items
[23] array · 3 items
[24] array · 3 items
[25] array · 3 items
[26] array · 1 item
[27] array · 3 items
[28] array · 3 items
[29] array · 3 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 10 items
[0] array · 3 items
[1] array · 4 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 1 item
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 3 items
[1] array · 3 items
[2] array · 5 items
[3] array · 3 items
[4] array · 5 items
[5] array · 3 items
[6] array · 5 items
[7] array · 3 items
[8] array · 5 items
[9] array · 3 items
[10] array · 5 items
[11] array · 3 items
[12] array · 5 items
[13] array · 3 items
[14] array · 5 items
[15] array · 3 items
[16] array · 3 items
[17] array · 5 items
[18] array · 3 items
[19] array · 5 items
[20] array · 3 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 13 items
[0] array · 3 items
[1] array · 4 items
[2] array · 5 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 · 5 items
[12] array · 5 items
gaps array · 0 items
analysis object · 4 fields
methods array · 1 item
[0] 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 · 0 items
resolved_accessions array · 0 items
statements array · 0 items
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 5 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 · 1 item
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 · 5 items
assays array · 2 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 · 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:34590792", "kind": "science-record", "revision": 4, "content_hash": "sha256:7df52b7f38fbf856c7abdcd704e2eac5a5ab639b0932f608d7ddf695f8640a5e", "created_at": "2026-11-01T15:41:54Z", "updated_at": "2026-11-01T21:26:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SEC61G overexpression and DNA amplification correlates with prognosis and immune cell infiltration in head and neck squamous cell carcinoma.", "doi": "10.1002/cam4.4301", "pmid": "34590792", "authors": ["Tianzhu Lu", "Yiping Chen", "Xiaochang Gong", "Qiaojuan Guo", "Canyang Lin", "Qingfeng Luo", "Ziwei Tu", "Jianji Pan", "Jingao Li"], "journal": "Cancer medicine", "year": 2021, "abstract": "BACKGROUND: The SEC61 translocon gamma subunit (SEC61G) is a component of the SEC61 complex, which import protein into the endoplasmic reticulum. However, the correlation between SEC61G and disease prognosis in head and neck squamous cell carcinoma (HNSCC) remains unclear.\nMETHODS: SEC61G expression was analyzed using publicly available datasets. The association between SEC61G and disease prognosis was evaluated. SEC61G methylation and copy number variation were investigated and gene set enrichment analysis and gene ontology analyses identified SEC61G-associated functions. We also investigated the correlation between SEC61G and immune cell infiltration. Finally, immunohistochemistry was used to detect SEC61G expression in oropharyngeal carcinoma.\nRESULTS: SEC61G was overexpressed in pan-cancers, including HNSCC, and negatively correlated with overall survival (OS) (p < 0.001 for TCGA-HNSCC and p = 0.019 for GSE65858). Moreover, SEC61G was an independent prognostic factor for OS in TCGA and GSE65858 [hazard ratio (HR) = 1.80, 95% CI: 1.35-2.39, p < 0.001; HR = 1.87, 95% CI: 1.14-3.07, p = 0.013, respectively). SEC61G DNA amplification (9.66% of patients) was significantly associated with poor OS (p = 0.034). SEC61G overexpression and DNA amplification negatively correlated with B cell (p < 0.001), CD8+ T cell (p < 0.001), CD4+ T cell (p < 0.001), macrophage (p < 0.05), neutrophil (p < 0.001), and dendritic cell infiltration (p < 0.001). Among patients with metastatic urothelial cancer received atezolizumab, patients with high SEC61G expression had an inferior OS (p = 0.006). Furthermore, SEC61G protein expression was also an independent prognostic factor of OS (HR = 2.46, 95% CI: 1.15-5.28, p = 0.021) and progression-free survival (HR = 2.82, 95% CI: 1.36-5.85, p = 0.005) for oropharyngeal cancer.\nCONCLUSIONS: SEC61G is overexpressed in HNSCC and is an independent prognostic factor for OS. SEC61G DNA amplification contributes to overexpression and poor outcome. Interestingly, SEC61G correlates with immune cell infiltration in HNSCC. These findings suggest that SEC61G is a potential broad-spectrum biomarker for prognosis in HNSCC.", "claims": [{"id": "claim-method", "statement": "Survival curves were drawn using the Kaplan–Meier method, and the differences between groups were assessed via the log‐rank test or Breslow test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34590792", "locator": "sections[9] \"Statistical analyses\" paragraph 2", "quote": "Survival curves were drawn using the Kaplan–Meier method, and the differences between groups were assessed via the log‐rank test or Breslow test."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34590792"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34590792", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.4301", "sha256": "sha256:7b8d3e989e3b97a64667dfc2bcf2e9b40560a642181a0ab8c9d77430145158fc", "bytes": 37466, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.4301", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8559468", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:34590792:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5cc9bede9f6e5131691756b5e3f41d579890d886a13be2108f040cd016d18bb2", "bytes": 1077, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#cam44301-tbl-0001", "version": null, "note": "Demographic and clinical characteristics of HNSCC patients in TCGA and GSE65858", "structure": {"pmcid": "PMC8559468", "section_index": 3, "section_title": "Data availability", "row_count": 30, "column_count": 3}, "table": {"label": "TABLE 1", "caption": "Demographic and clinical characteristics of HNSCC patients in TCGA and GSE65858", "rows": [["Characteristics", "TCGA", "GSE65858"], ["n (%)", "n (%)"], ["Gender"], ["Female", "126 (27.7)", "43 (17.4)"], ["Male", "329 (72.3)", "223 (82.6)"], ["Age (year)"], ["<60", "216 (47.5)", "153 (56.7)"], ["≥60", "329 (52.5)", "117 (43.3)"], ["HPV"], ["Negative", "378 (83.1)", "197 (73.0)"], ["Positive", "77 (16.9)", "73 (27.0)"], ["T classification"], ["T1", "30 (6.6)", "35 (13.0)"], ["T2", "128 (28.1)", "80 (29.6)"], ["T3", "127 (27.9)", "58 (21.5)"], ["T4", "170 (37.4)", "97 (35.9)"], ["N classification"], ["N0", "227 (49.9)", "94 (34.8)"], ["N1", "80 (17.6)", "32 (11.9)"], ["N2", "141 (31.0)", "132 (48.9)"], ["N3", "7 (1.5)", "12 (4.4)"], ["Clinical stage"], ["Ⅰ", "17 (3.7)", "18 (6.7)"], ["Ⅱ", "85 (18.7)", "37 (13.7)"], ["Ⅲ", "99 (21.8)", "37 (13.7)"], ["Ⅳ", "254 (55.8)", "178 (65.9)"], ["Histologic grade"], ["G1", "52 (11.4)", ""], ["G2", "286 (62.9)", ""], ["G3", "117 (25.7)", ""]], "row_count": 30, "column_count": 3, "numeric_cells": 42, "header_rows": 2, "locator": "section[3]/table-wrap[1]#cam44301-tbl-0001"}}, {"id": "asset:table:pmid:34590792:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f4466135341a9cde72e01e7eb0bd9e5a7ec9b320547a5ec4869dcc979fa380bc", "bytes": 982, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#cam44301-tbl-0002", "version": null, "note": "The multivariate analysis of overall survival according to SEC61G expression, after adjusting for other potential predictors in TCGA and GSE65858", "structure": {"pmcid": "PMC8559468", "section_index": 12, "section_title": "SEC61G overexpression correlates with poor overall survival in HNSCC", "row_count": 10, "column_count": 5}, "table": {"label": "TABLE 2", "caption": "The multivariate analysis of overall survival according to SEC61G expression, after adjusting for other potential predictors in TCGA and GSE65858", "rows": [["Characteristics", "TCGA", "GSE65858"], ["HR (95% CI)", "p‐value", "HR (95% CI)", "p‐value"], ["Gender (Female vs. Male)", "0.81 (0.59–1.09)", "0.163", "1.01 (0.58–1.74)", "0.990"], ["Age (<60 years vs. ≥60 years)", "1.14 (0.86–1.53)", "0.362", "1.31 (0.86–2.01)", "0.214"], ["HPV (Negative vs. Positive)", "0.93 (0.61–1.41)", "0.744", "0.47 (0.28–0.83)", "0.009"], ["Histologic grade"], ["G1 versus G2", "1.86 (1.14–3.03)", "0.013", "", ""], ["G1 versus G3", "1.56 (0.92–2.63)", "0.100", "", ""], ["Clinical stage (I–II vs. III–IV)", "1.24 (0.87–2.63)", "0.231", "1.78 (1.30–2.44)", "<0.001"], ["SEC61G (Low vs. High)", "1.80 (1.35–2.39)", "<0.001", "1.87 (1.14–3.07)", "0.013"]], "row_count": 10, "column_count": 5, "numeric_cells": 29, "header_rows": 2, "locator": "section[12]/table-wrap[1]#cam44301-tbl-0002"}}, {"id": "asset:table:pmid:34590792:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:17df43048521beffae296494841562e095ad5cc2fe5d10b99f4ff6d37104e405", "bytes": 965, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#cam44301-tbl-0003", "version": null, "note": "Demographic and clinical characteristics of oropharyngeal cancer patients with negative and positive SEC61G", "structure": {"pmcid": "PMC8559468", "section_index": 17, "section_title": "SEC61G is upregulated and correlated with adverse outcome in oropharyngeal cancer", "row_count": 21, "column_count": 5}, "table": {"label": "TABLE 3", "caption": "Demographic and clinical characteristics of oropharyngeal cancer patients with negative and positive SEC61G", "rows": [["Categories", "Level", "SEC61G expression"], ["Negative (n = 33)", "Positive (n = 58)", "p‐value"], ["Gender", "Female", "6", "5", "0.197"], ["Male", "27", "53"], ["Age (year)", "<60", "18", "34", "0.706"], ["≥60", "15", "24"], ["T classification", "T1–T2", "18", "29", "0.737"], ["T3–T4", "15", "28"], ["N classification", "N0–1", "11", "15", "0.448"], ["N2–3", "22", "43"], ["Clinical stage", "I–II", "4", "16", "0.087"], ["III–IV", "29", "42"], ["Smoking", "No", "11", "22", "0.513"], ["Yes", "21", "31"], ["Differentiated", "Poor", "9", "8", "0.193"], ["Moderately", "17", "30"], ["Well", "7", "20"], ["Keratinization", "No", "14", "10", "0.009"], ["Yes", "19", "48"], ["Treatment", "RT ± CT", "21", "31", "0.345"], ["Surgery ± RT ± CT", "12", "27"]], "row_count": 21, "column_count": 5, "numeric_cells": 54, "header_rows": 2, "locator": "section[17]/table-wrap[1]#cam44301-tbl-0003"}}, {"id": "asset:table:pmid:34590792:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:620e3a01ea8e433d24983ae8e378a74beedb76243bef15f1222ade73709aa063", "bytes": 1367, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#cam44301-tbl-0004", "version": null, "note": "The multivariate analysis of overall survival and progression‐free survival according to SEC61G expression, after adjusting for other potential predictors in oropharyngeal cancer", "structure": {"pmcid": "PMC8559468", "section_index": 17, "section_title": "SEC61G is upregulated and correlated with adverse outcome in oropharyngeal cancer", "row_count": 13, "column_count": 5}, "table": {"label": "TABLE 4", "caption": "The multivariate analysis of overall survival and progression‐free survival according to SEC61G expression, after adjusting for other potential predictors in oropharyngeal cancer", "rows": [["Characteristics", "OS", "PFS"], ["HR (95% CI)", "p value", "HR (95% CI)", "p value"], ["Gender (Female vs. Male)", "0.83 (0.22–3.16)", "0.780", "0.85 (0.23–3.12)", "0.808"], ["Age (≤60 vs. >60)", "2.52 (1.27–5.00)", "0.008", "2.16 (1.14–4.09)", "0.018"], ["Clinical stage (Ⅰ–Ⅱ vs. Ⅲ–Ⅳ)", "4.02 (1.37–11.83)", "0.012", "2.86 (1.17–7.00)", "0.021"], ["Smoking (No vs. Yes)", "1.67 (0.70–3.975)", "0.243", "1.67 (0.74–3.77)", "0.213"], ["Treatment (RT ± CT vs. Surgery ± RT ± CT)", "0.46 (0.23–3.91)", "0.025", "0.57 (0.30–1.08)", "0.085"], ["Differentiated", "", "0.848", "", "0.348"], ["(Poor vs. moderately)", "0.75 (0.23–2.49)", "0.637", "0.48 (0.17–1.35)", "0.165"], ["(Poor vs. well)", "0.87 (0.25–3.09)", "0.831", "0.46 (0.15–1.39)", "0.171"], ["Keratinization (No vs. yes)", "2.91 (0.77–11.03)", "0.105", "3.20 (0.98–10.48)", "0.054"], ["SEC61G (Negative vs. positive)", "2.46 (1.15–5.28)", "0.021", "2.82 (1.36–5.85)", "0.005"], ["P16 (Negative vs. positive)", "0.92 (0.29–2.91)", "0.886", "1.02 (0.34–3.03)", "0.971"]], "row_count": 13, "column_count": 5, "numeric_cells": 47, "header_rows": 2, "locator": "section[17]/table-wrap[2]#cam44301-tbl-0004"}}], "gaps": []}, "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": "Survival curves were drawn using the Kaplan–Meier method, and the differences between groups were assessed via the log‐rank test or Breslow test."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:34590792", "asset:table:pmid:34590792:1", "asset:table:pmid:34590792:2", "asset:table:pmid:34590792:3", "asset:table:pmid:34590792:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:50:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 9730, "completion_tokens": 390, "cached_tokens": 256}}, "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:34590792", "type": "paper", "label": "pmid:34590792"}, {"id": "source:pmid:34590792", "type": "manuscript", "label": "PMID 34590792 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34590792", "type": "paper", "label": "pmid:34590792"}, {"id": "source:pmid:34590792", "type": "manuscript", "label": "PMID 34590792 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34590792", "type": "extraction", "used": ["source:pmid:34590792"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:34590792", "parent_hash": "sha256:934a981cadf4d4f0be7c6dbabe7a5fe683049ad4a12d04acb4ed427768906aea", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["EC61G and immune cell infiltration. Finally, immunohistochemistry was used to detect SEC61G expression in orop"], "order_basis": "paper_text_order:767", "id": "assay:1"}, {"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": ["Survival curves were drawn using the Kaplan–Meier method, and the differences between groups were assessed via the log‐rank test or Breslow test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}