A Novel Clinical Six-Flavoprotein-Gene Signature Predicts Prognosis in Esophageal Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31815134", "kind": "science-record", "revision": 7, "content_hash": "sha256:08417ed75fd04a04affad9bbf776af96d714da8f041025efc6a2b45e6ce44959", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:01:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Novel Clinical Six-Flavoprotein-Gene Signature Predicts Prognosis in Esophageal Squamous Cell Carcinoma.", "doi": "10.1155/2019/3869825", "pmid": "31815134", "authors": ["Liu Peng", "Jin-Cheng Guo", "Lin Long", "Feng Pan", "Jian-Mei Zhao", "Li-Yan Xu", "En-Min Li"], "journal": "BioMed research international", "year": 2019, "abstract": "Flavoproteins and their interacting proteins play important roles in mitochondrial electron transport, fatty acid degradation, and redox regulation. However, their clinical significance and function in esophageal squamous cell carcinoma (ESCC) are little known. Here, using survival analysis and machine learning, we mined 179 patient expression profiles with ESCC in GSE53625 from the Gene Expression Omnibus (GEO) database and constructed a signature consisting of two flavoprotein genes (GPD2 and PYROXD2) and four flavoprotein interacting protein genes (CTTN, GGH, SRC, and SYNJ2BP). Kaplan-Meier analysis revealed the signature was significantly associated with the survival of ESCC patients (mean survival time: 26.77 months in the high-risk group vs. 54.97 months in the low-risk group, P < 0.001, n = 179), and time-dependent ROC analysis demonstrated that the six-gene signature had good predictive ability for six-year survival for ESCC (AUC = 0.86, 95% CI: 0.81-0.90). We then validated its prediction performance in an independent set by RT-PCR (mean survival: 15.73 months in the high-risk group vs. 21.1 months in the low-risk group, P=0.032, n = 121). Furthermore, RNAi-mediated knockdown of genes in the flavoprotein signature led to decreased proliferation and migration of ESCC cells. Taken together, CTTN, GGH, GPD2, PYROXD2, SRC, and SYNJ2BP have an important clinical significance for prognosis of ESCC patients, suggesting they are efficient prognostic markers and potential targets for ESCC therapy.", "claims": [{"id": "claim-data-access", "statement": "No data were used to support this study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31815134", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "No data were used to support this study."}], "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:31815134"], "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:GSE53625"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE53625"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31815134", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2019/3869825", "sha256": "sha256:91922a5f453528c52f36f8f4747aeba6e79921c5e035be62b54cbebc1042b819", "bytes": 45109, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2019/3869825", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6878914", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53625", "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=GSE53625", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53625", "version": null, "note": "No data were used to support this study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No data were used to support this study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1296956", "GSM1296957", "GSM1296958", "GSM1296959", "GSM1296960", "GSM1296961", "GSM1296962", "GSM1296963", "GSM1296964", "GSM1296965", "GSM1296966", "GSM1296967", "GSM1296968", "GSM1296969", "GSM1296970", "GSM1296971", "GSM1296972", "GSM1296973", "GSM1296974", "GSM1296975", "GSM1296976", "GSM1296977", "GSM1296978", "GSM1296979", "GSM1296980", "GSM1296981", "GSM1296982", "GSM1296983", "GSM1296984", "GSM1296985", "GSM1296986", "GSM1296987", "GSM1296988", "GSM1296989", "GSM1296990", "GSM1296991", "GSM1296992", "GSM1296993", "GSM1296994", "GSM1296995", "GSM1296996", "GSM1296997", "GSM1296998", "GSM1296999", "GSM1297000", "GSM1297001", "GSM1297002", "GSM1297003", "GSM1297004", "GSM1297005", "GSM1297006", "GSM1297007", "GSM1297008", "GSM1297009", "GSM1297010", "GSM1297011", "GSM1297012", "GSM1297013", "GSM1297014", "GSM1297015", "GSM1297016", "GSM1297017", "GSM1297018", "GSM1297019", "GSM1297020", "GSM1297021", "GSM1297022", "GSM1297023", "GSM1297024", "GSM1297025", "GSM1297026", "GSM1297027", "GSM1297028", "GSM1297029", "GSM1297030", "GSM1297031", "GSM1297032", "GSM1297033", "GSM1297034", "GSM1297035", "GSM1297036", "GSM1297037", "GSM1297038", "GSM1297039", "GSM1297040", "GSM1297041", "GSM1297042", "GSM1297043", "GSM1297044", "GSM1297045", "GSM1297046", "GSM1297047", "GSM1297048", "GSM1297049", "GSM1297050", "GSM1297051", "GSM1297052", "GSM1297053", "GSM1297054", "GSM1297055", "GSM1297056", "GSM1297057", "GSM1297058", "GSM1297059", "GSM1297060", "GSM1297061", "GSM1297062", "GSM1297063", "GSM1297064", "GSM1297065", "GSM1297066", "GSM1297067", "GSM1297068", "GSM1297069", "GSM1297070", "GSM1297071", "GSM1297072", "GSM1297073", "GSM1297074", "GSM1297075", "GSM1297076", "GSM1297077", "GSM1297078", "GSM1297079", "GSM1297080", "GSM1297081", "GSM1297082", "GSM1297083", "GSM1297084", "GSM1297085", "GSM1297086", "GSM1297087", "GSM1297088", "GSM1297089", "GSM1297090", "GSM1297091", "GSM1297092", "GSM1297093", "GSM1297094", "GSM1297095", "GSM1297096", "GSM1297097", "GSM1297098", "GSM1297099", "GSM1297100", "GSM1297101", "GSM1297102", "GSM1297103", "GSM1297104", "GSM1297105", "GSM1297106", "GSM1297107", "GSM1297108", "GSM1297109", "GSM1297110", "GSM1297111", "GSM1297112", "GSM1297113", "GSM1297114", "GSM1297115", "GSM1297116", "GSM1297117", "GSM1297118", "GSM1297119", "GSM1297120", "GSM1297121", "GSM1297122", "GSM1297123", "GSM1297124", "GSM1297125", "GSM1297126", "GSM1297127", "GSM1297128", "GSM1297129", "GSM1297130", "GSM1297131", "GSM1297132", "GSM1297133", "GSM1297134", "GSM1297135", "GSM1297136", "GSM1297137", "GSM1297138", "GSM1297139", "GSM1297140", "GSM1297141", "GSM1297142", "GSM1297143", "GSM1297144", "GSM1297145", "GSM1297146", "GSM1297147", "GSM1297148", "GSM1297149", "GSM1297150", "GSM1297151", "GSM1297152", "GSM1297153", "GSM1297154", "GSM1297155", "GSM1297156", "GSM1297157", "GSM1297158", "GSM1297159", "GSM1297160", "GSM1297161", "GSM1297162", "GSM1297163", "GSM1297164", "GSM1297165", "GSM1297166", "GSM1297167", "GSM1297168", "GSM1297169", "GSM1297170", "GSM1297171", "GSM1297172", "GSM1297173", "GSM1297174", "GSM1297175", "GSM1297176", "GSM1297177", "GSM1297178", "GSM1297179", "GSM1297180", "GSM1297181", "GSM1297182", "GSM1297183", "GSM1297184", "GSM1297185", "GSM1297186", "GSM1297187", "GSM1297188", "GSM1297189", "GSM1297190", "GSM1297191", "GSM1297192", "GSM1297193", "GSM1297194", "GSM1297195", "GSM1297196", "GSM1297197", "GSM1297198", "GSM1297199", "GSM1297200", "GSM1297201", "GSM1297202", "GSM1297203", "GSM1297204", "GSM1297205", "GSM1297206", "GSM1297207", "GSM1297208", "GSM1297209", "GSM1297210", "GSM1297211", "GSM1297212", "GSM1297213", "GSM1297214", "GSM1297215", "GSM1297216", "GSM1297217", "GSM1297218", "GSM1297219", "GSM1297220", "GSM1297221", "GSM1297222", "GSM1297223", "GSM1297224", "GSM1297225", "GSM1297226", "GSM1297227", "GSM1297228", "GSM1297229", "GSM1297230", "GSM1297231", "GSM1297232", "GSM1297233", "GSM1297234", "GSM1297235", "GSM1297236", "GSM1297237", "GSM1297238", "GSM1297239", "GSM1297240", "GSM1297241", "GSM1297242", "GSM1297243", "GSM1297244", "GSM1297245", "GSM1297246", "GSM1297247", "GSM1297248", "GSM1297249", "GSM1297250", "GSM1297251", "GSM1297252", "GSM1297253", "GSM1297254", "GSM1297255", "GSM1297256", "GSM1297257", "GSM1297258", "GSM1297259", "GSM1297260", "GSM1297261", "GSM1297262", "GSM1297263", "GSM1297264", "GSM1297265", "GSM1297266", "GSM1297267", "GSM1297268", "GSM1297269", "GSM1297270", "GSM1297271", "GSM1297272", "GSM1297273", "GSM1297274", "GSM1297275", "GSM1297276", "GSM1297277", "GSM1297278", "GSM1297279", "GSM1297280", "GSM1297281", "GSM1297282", "GSM1297283", "GSM1297284", "GSM1297285", "GSM1297286", "GSM1297287", "GSM1297288", "GSM1297289", "GSM1297290", "GSM1297291", "GSM1297292", "GSM1297293", "GSM1297294", "GSM1297295", "GSM1297296", "GSM1297297", "GSM1297298", "GSM1297299", "GSM1297300", "GSM1297301", "GSM1297302", "GSM1297303", "GSM1297304", "GSM1297305", "GSM1297306", "GSM1297307", "GSM1297308", "GSM1297309", "GSM1297310", "GSM1297311", "GSM1297312", "GSM1297313"], "sample_count": 358, "group_sizes": null, "group_sizes_basis": null, "platform": "18109", "taxon": "Homo sapiens", "title": "LncRNA profile study reveals a three-lncRNA signature associated with the survival of esophageal squamous cell carcinoma patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31815134:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dc6a417a4f9ec1b437ef0c36fc50e12a24cf7db1e8d3255eb3458234ea2a4dff", "bytes": 485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#tab1", "version": null, "note": "Clinical characteristics of 121 ESCC patients used for validation experiments.", "structure": {"pmcid": "PMC6878914", "section_index": 6, "section_title": "2.4. Tissue Sample Collection", "row_count": 16, "column_count": 2}, "table": {"label": "Table 1", "caption": "Clinical characteristics of 121 ESCC patients used for validation experiments.", "rows": [["Clinical parameters", "Number"], ["Total cases", "121"], ["Status"], ["Deceased", "54"], ["Living", "67"], ["Mean age, year", "57.8"], ["Age"], ["<57.8", "62"], ["≥57.8", "59"], ["Gender"], ["Male", "92"], ["Female", "29"], ["pTNM stage"], ["I", "6"], ["II", "57"], ["III", "58"]], "row_count": 16, "column_count": 2, "numeric_cells": 13, "header_rows": 1, "locator": "section[6]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:31815134:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dc4e0e565b52e84a42db53980db2803d3d98c2b9d301c59565129c622dafa795", "bytes": 1097, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#tab2", "version": null, "note": "Primer sequences for qRT-PCR and siRNA sequences.", "structure": {"pmcid": "PMC6878914", "section_index": 7, "section_title": "2.5. RNA Extraction, cDNA Synthesis, and qRT-PCR", "row_count": 24, "column_count": 2}, "table": {"label": "Table 2", "caption": "Primer sequences for qRT-PCR and siRNA sequences.", "rows": [["Gene", "Sequence (5′-3′)"], ["", "Primers for qRT-PCR"], ["CTTN-qF", "AACGATCTGGGGATCACAGC"], ["CTTN-qR", "CCAGCCGTCGTCAATCATC T"], ["PXROXD2-qF", "CAAGCTCAGCCACCACACAT"], ["PXROXD2-qR", "GCTTCTCACCTCTGTGCCAT"], ["SYNJ2BP-qF", "CTGCACCAGGATGCTGTAGAC"], ["SYNJ2BP-qR", "GAAAGCCCAGGCTGCTACCAT"], ["GGH-qF", "GATGGCATTTCCCATGCACC"], ["GGH-qR", "TGCTTTCTCCTCTTCAGATTCAG"], ["GPD2-qF", "GTGGCCAAAATGGCAAGTGT"], ["GPD2-qR", "AATCCTGGGTAGGGCTTCCT"], ["SRC-qF", "GTGGGAGAGAACCTGGTGTG"], ["SRC-qR", "GATGGTGAAGCGGCCATAGA"], ["ACTB-qF", "CAACTGGGACGACATGGAGAAA"], ["ACTB-qR", "GATAGCAACGTACATGGCTGGG"], ["", "siRNA target sequence"], ["CTTN-Homo-449", "CCAUGGCUAUGGAGGGAAATT"], ["PYROXD2-Homo-1328", "CCUCCUUCAUCAGGCCUUUTT"], ["SYNJ2BP-Homo-2746", "GGACAAGUUGAAGACCCUUTT"], ["GGH-Homo-338", "GCGAGCCUCGAGCUGUCUATT"], ["GPD2-Homo-494", "GCAUUUCAGAACCAGUUAATT"], ["SRC-Homo-937", "GCCUCUCAGUGUCUGACUUTT"], ["Negative control", "UUCUCCGAACGUGUCACGUTT"]], "row_count": 24, "column_count": 2, "numeric_cells": 7, "header_rows": 1, "locator": "section[7]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:31815134:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:461831c5810638504772db26c23d89139d153419dc6c5a792e7b8694b8812d79", "bytes": 1137, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tab3", "version": null, "note": "Identities of flavoproteins and their interacting proteins in the prognostic expression signature and their univariate Cox association with prognosis.", "structure": {"pmcid": "PMC6878914", "section_index": 15, "section_title": "3.2. Selection of Flavoproteins and Interacting Protein Combinations for the Prognostic Signature in the Training Dataset", "row_count": 7, "column_count": 7}, "table": {"label": "Table 3", "caption": "Identities of flavoproteins and their interacting proteins in the prognostic expression signature and their univariate Cox association with prognosis.", "rows": [["Ensembl ID", "Gene symbol", "Gene description", "Coefficienta", "P valuea", "Gene expression level association with prognosis", "Chromosome location"], ["ENSG00000115159", "GPD2", "Glycerol-3-phosphate dehydrogenase 2", "−0.77", "0.01", "Low", "2 : 156435290–156613735 : 1"], ["ENSG00000119943", "PYROXD2", "Pyridine nucleotide-disulphide oxidoreductase domain 2", "0.28", "0.00", "High", "10 : 98383565–98415184 : −1"], ["ENSG00000085733", "CTTN", "Cortactin", "0.33", "0.00", "High", "11 : 70398404–70436584 : 1"], ["ENSG00000137563", "GGH", "Gamma-glutamyl hydrolase", "−0.39", "0.01", "Low", "8 : 63015079–63039171 : −1"], ["ENSG00000197122", "SRC", "Non-receptor tyrosine kinase", "0.54", "0.02", "High", "20 : 37344685–37406050 : 1"], ["ENSG00000213463", "SYNJ2BP", "Synaptojanin 2 binding protein", "0.48", "0.02", "High", "14 : 70366496–70417061 : −1"]], "row_count": 7, "column_count": 7, "numeric_cells": 27, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tab3"}}], "gaps": ["asset:data:geo:GSE53625 not downloaded", "asset:data:geo:GSE53625 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t test"}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_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": ["GSE53625"], "resolved_accessions": ["GSE53625"], "statements": ["No data were used to support this study."], "basis": "The paper names GSE53625 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": [], "assets": ["source:pmid:31815134", "data:geo:GSE53625", "asset:table:pmid:31815134:1", "asset:table:pmid:31815134:2", "asset:table:pmid:31815134:3"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE53625"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:53:40Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 37470, "completion_tokens": 1199, "cached_tokens": 792}}, "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:31815134", "type": "paper", "label": "pmid:31815134"}, {"id": "source:pmid:31815134", "type": "manuscript", "label": "PMID 31815134 full text"}, {"id": "data:geo:GSE53625", "type": "dataset", "label": "GEO GSE53625"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31815134", "type": "paper", "label": "pmid:31815134"}, {"id": "source:pmid:31815134", "type": "manuscript", "label": "PMID 31815134 full text"}, {"id": "data:geo:GSE53625", "type": "dataset", "label": "GEO GSE53625"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31815134", "type": "extraction", "used": ["source:pmid:31815134"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE53625", "type": "accession_resolution", "used": ["data:geo:GSE53625"], "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:31815134", "parent_hash": "sha256:eb7ae290f616fe0b77894ccb6dcee65b782cbeeae1d9deb13fe467b5a9378871", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE53625 licence not read", "asset:data:geo:GSE53625 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["=0.032, n = 121). Furthermore, RNAi-mediated knockdown of genes in the flavoprotein signature led t", "4 h until 70–80% confluence. ESCC cells were transfected with 30 nM or 75 nM siRNA using Lipofectamin", "C cells were transfected with 30 nM or 75 nM siRNA using Lipofectamine 3000 (Invitrogen) accord", "SRC, and SYNJ2BP and a negative control (NC) siRNA were synthesized by GenePharma (Suzhou, Jian"], "order_basis": "paper_text_order:1256", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Student's t test"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}