Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34630524", "kind": "science-record", "revision": 5, "content_hash": "sha256:e47b3bc0d0e875d9ead553f13bc824ade40958a367eb5b3b4eda4665de331cef", "created_at": "2026-11-01T17:36:16Z", "updated_at": "2026-11-01T22:47:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer.", "doi": "10.3389/fgene.2021.733715", "pmid": "34630524", "authors": ["Jing Yu", "Lei-Lei Liang", "Jing Liu", "Ting-Ting Liu", "Jian Li", "Lin Xiu", "Jia Zeng", "Tian-Tian Wang", "Di Wang", "Li-Jun Liang", "Da-Wei Xie", "Ding-Xiong Chen", "Ju-Sheng An", "Ling-Ying Wu"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Background: 5-Methylcytidine (m5C) is the most common RNA modification and plays an important role in multiple tumors including cervical cancer (CC). We aimed to develop a novel gene signature by identifying m5C modification subtypes of CC to better predict the prognosis of patients. Methods: We obtained the expression of 13 m5C regulatory factors from The Cancer Genome Atlas (TCGA all set, 257 patients) to determine m5C modification subtypes by the \"nonnegative matrix factorization\" (NMF). Then the \"limma\" package was used to identify differentially expressed genes (DEGs) between different subtypes. According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients). We also verified the risk prediction effect of gene signature in TCGA test set (129 patients), TCGA all set (257 patients) and GSE44001 (300 patients). Furthermore, a nomogram including this gene signature and clinicopathological parameters was established to predict the individual survival rate. Finally, the expression and function of these signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, colony formation, migration and invasion assays. Results: Based on consistent clustering of 13 m5C-modified genes, CC was divided into two subtypes (C1 and C2) and the C1 subtype had a worse prognosis. The 4-gene signature comprising FNDC3A, VEGFA, OPN3 and CPE was constructed. In TCGA training set and three validation sets, we found the prognosis of patients in the low-risk group was much better than that in the high-risk group. A nomogram incorporating the gene signature and T stage was constructed, and the calibration plot suggested that it could accurately predict the survival rate. The expression levels of FNDC3A, VEGFA, OPN3 and CPE were all high in cervical cancer tissues. Downregulation of FNDC3A, VEGFA or CPE expression suppressed the proliferation, migration and invasion of SiHa cells. Conclusions: Two m5C modification subtypes of CC were identified and then a 4-gene signature was established, which provide new feasible methods for clinical risk assessment and targeted therapies for CC.", "claims": [{"id": "claim-method", "statement": "According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34630524", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34630524", "locator": "sections[31] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified two m5C modification subtypes of cervical cancer and established a four-gene prognostic signature comprising FNDC3A, VEGFA, OPN3 and CPE.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34630524", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Two m5C modification subtypes of CC were identified and then a 4-gene signature was established, which provide new feasible methods for clinical risk assessment and targeted therapies for CC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified two m5C modification subtypes of cervical cancer and established a four-gene prognostic signature comprising FNDC3A, VEGFA, OPN3 and CPE.", "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:34630524"], "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:GSE44001"], "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:GSE44001"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34630524", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2021.733715", "sha256": "sha256:be9695d5590a900961dcfbb77b148e4fd8ef50c6aa39a5f0cdc15497e2d83264", "bytes": 53635, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2021.733715", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8493221", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE44001", "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=GSE44001", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE44001", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1076341", "GSM1076342", "GSM1076343", "GSM1076344", "GSM1076345", "GSM1076346", "GSM1076347", "GSM1076348", "GSM1076349", "GSM1076350", "GSM1076351", "GSM1076352", "GSM1076353", "GSM1076354", "GSM1076355", "GSM1076356", "GSM1076357", "GSM1076358", "GSM1076359", "GSM1076360", "GSM1076361", "GSM1076362", "GSM1076363", "GSM1076364", "GSM1076365", "GSM1076366", "GSM1076367", "GSM1076368", "GSM1076369", "GSM1076370", "GSM1076371", "GSM1076372", "GSM1076373", "GSM1076374", "GSM1076375", "GSM1076376", "GSM1076377", "GSM1076378", "GSM1076379", "GSM1076380", "GSM1076381", "GSM1076382", "GSM1076383", "GSM1076384", "GSM1076385", "GSM1076386", "GSM1076387", "GSM1076388", "GSM1076389", "GSM1076390", "GSM1076391", "GSM1076392", "GSM1076393", "GSM1076394", "GSM1076395", "GSM1076396", "GSM1076397", "GSM1076398", "GSM1076399", "GSM1076400", "GSM1076401", "GSM1076402", "GSM1076403", "GSM1076404", "GSM1076405", "GSM1076406", "GSM1076407", "GSM1076408", "GSM1076409", "GSM1076410", "GSM1076411", "GSM1076412", "GSM1076413", "GSM1076414", "GSM1076415", "GSM1076416", "GSM1076417", "GSM1076418", "GSM1076419", "GSM1076420", "GSM1076421", "GSM1076422", "GSM1076423", "GSM1076424", "GSM1076425", "GSM1076426", "GSM1076427", "GSM1076428", "GSM1076429", "GSM1076430", "GSM1076431", "GSM1076432", "GSM1076433", "GSM1076434", "GSM1076435", "GSM1076436", "GSM1076437", "GSM1076438", "GSM1076439", "GSM1076440", "GSM1076441", "GSM1076442", "GSM1076443", "GSM1076444", "GSM1076445", "GSM1076446", "GSM1076447", "GSM1076448", "GSM1076449", "GSM1076450", "GSM1076451", "GSM1076452", "GSM1076453", "GSM1076454", "GSM1076455", "GSM1076456", "GSM1076457", "GSM1076458", "GSM1076459", "GSM1076460", "GSM1076461", "GSM1076462", "GSM1076463", "GSM1076464", "GSM1076465", "GSM1076466", "GSM1076467", "GSM1076468", "GSM1076469", "GSM1076470", "GSM1076471", "GSM1076472", "GSM1076473", "GSM1076474", "GSM1076475", "GSM1076476", "GSM1076477", "GSM1076478", "GSM1076479", "GSM1076480", "GSM1076481", "GSM1076482", "GSM1076483", "GSM1076484", "GSM1076485", "GSM1076486", "GSM1076487", "GSM1076488", "GSM1076489", "GSM1076490", "GSM1076491", "GSM1076492", "GSM1076493", "GSM1076494", "GSM1076495", "GSM1076496", "GSM1076497", "GSM1076498", "GSM1076499", "GSM1076500", "GSM1076501", "GSM1076502", "GSM1076503", "GSM1076504", "GSM1076505", "GSM1076506", "GSM1076507", "GSM1076508", "GSM1076509", "GSM1076510", "GSM1076511", "GSM1076512", "GSM1076513", "GSM1076514", "GSM1076515", "GSM1076516", "GSM1076517", "GSM1076518", "GSM1076519", "GSM1076520", "GSM1076521", "GSM1076522", "GSM1076523", "GSM1076524", "GSM1076525", "GSM1076526", "GSM1076527", "GSM1076528", "GSM1076529", "GSM1076530", "GSM1076531", "GSM1076532", "GSM1076533", "GSM1076534", "GSM1076535", "GSM1076536", "GSM1076537", "GSM1076538", "GSM1076539", "GSM1076540", "GSM1076541", "GSM1076542", "GSM1076543", "GSM1076544", "GSM1076545", "GSM1076546", "GSM1076547", "GSM1076548", "GSM1076549", "GSM1076550", "GSM1076551", "GSM1076552", "GSM1076553", "GSM1076554", "GSM1076555", "GSM1076556", "GSM1076557", "GSM1076558", "GSM1076559", "GSM1076560", "GSM1076561", "GSM1076562", "GSM1076563", "GSM1076564", "GSM1076565", "GSM1076566", "GSM1076567", "GSM1076568", "GSM1076569", "GSM1076570", "GSM1076571", "GSM1076572", "GSM1076573", "GSM1076574", "GSM1076575", "GSM1076576", "GSM1076577", "GSM1076578", "GSM1076579", "GSM1076580", "GSM1076581", "GSM1076582", "GSM1076583", "GSM1076584", "GSM1076585", "GSM1076586", "GSM1076587", "GSM1076588", "GSM1076589", "GSM1076590", "GSM1076591", "GSM1076592", "GSM1076593", "GSM1076594", "GSM1076595", "GSM1076596", "GSM1076597", "GSM1076598", "GSM1076599", "GSM1076600", "GSM1076601", "GSM1076602", "GSM1076603", "GSM1076604", "GSM1076605", "GSM1076606", "GSM1076607", "GSM1076608", "GSM1076609", "GSM1076610", "GSM1076611", "GSM1076612", "GSM1076613", "GSM1076614", "GSM1076615", "GSM1076616", "GSM1076617", "GSM1076618", "GSM1076619", "GSM1076620", "GSM1076621", "GSM1076622", "GSM1076623", "GSM1076624", "GSM1076625", "GSM1076626", "GSM1076627", "GSM1076628", "GSM1076629", "GSM1076630", "GSM1076631", "GSM1076632", "GSM1076633", "GSM1076634", "GSM1076635", "GSM1076636", "GSM1076637", "GSM1076638", "GSM1076639", "GSM1076640"], "sample_count": 300, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Genetic profiling to predict recurrence of early cervical cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE44001 not downloaded", "asset:data:geo:GSE44001 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients)."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-4", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-5", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.8, "band": "high", "quote": "decision curve analysis"}}, {"id": "method-6", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE44001"], "resolved_accessions": ["GSE44001"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE44001 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": ["survival_km"], "assets": ["source:pmid:34630524", "data:geo:GSE44001"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE44001"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:03:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15791, "completion_tokens": 1052, "cached_tokens": 128}}, "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:34630524", "type": "paper", "label": "pmid:34630524"}, {"id": "source:pmid:34630524", "type": "manuscript", "label": "PMID 34630524 full text"}, {"id": "data:geo:GSE44001", "type": "dataset", "label": "GEO GSE44001"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34630524", "type": "paper", "label": "pmid:34630524"}, {"id": "source:pmid:34630524", "type": "manuscript", "label": "PMID 34630524 full text"}, {"id": "data:geo:GSE44001", "type": "dataset", "label": "GEO GSE44001"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34630524", "type": "extraction", "used": ["source:pmid:34630524"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE44001", "type": "accession_resolution", "used": ["data:geo:GSE44001"], "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:34630524", "parent_hash": "sha256:e5c37c55b5c56bd146640a5f674e9d0df2833477fd6260666f5ed3162f60d643", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE44001 licence not read", "asset:data:geo:GSE44001 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["se signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, colony formation, m", "e explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, colony formation, migrat"], "order_basis": "paper_text_order:1258", "id": "assay:1"}, {"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": ["l lead to better decisions. Cell Culture and Transfection The human CC cell line SiHa was provided by", "ditional file 1: Supplementary Table S3. The transfection method was described in our previous article", "O2 in a humidified incubator. Human specific siRNA sequences are shown in Additional file 1: Su"], "order_basis": "paper_text_order:3552", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e Cell Resource Center, IBMS, CAMS/PUMC. The cell lines were cultured in DMEM medium supplemented with 10% fetal b", "Center, IBMS, CAMS/PUMC. The cell lines were cultured in DMEM medium supplemented with 10% fetal bovi"], "order_basis": "paper_text_order:3656", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["According to these DEGs, we performed Cox regression and Kaplan-Meier (KM) survival analysis to establish a novel gene signature in TCGA training set (128 patients)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}