The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34827123", "kind": "science-record", "revision": 4, "content_hash": "sha256:6bb2137b98e4c10054bc75da885189506cbb289f4a352e4f934654dd4b676763", "created_at": "2026-11-01T17:36:32Z", "updated_at": "2026-11-01T22:05:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer.", "doi": "10.3390/biology10111130", "pmid": "34827123", "authors": ["Huimin Li", "Lin Chen", "Yunsong Han", "Fangfang Zhang", "Yanyan Wang", "Yali Han", "Yange Wang", "Qiang Wang", "Xiangqian Guo"], "journal": "Biology", "year": 2021, "abstract": "RNA modifications are reversible, dynamically regulated, and involved in a variety of diseases such as cancers. Given the lack of efficient and reliable biomarkers for early diagnosis of ovarian cancer (OV), this study was designed to explore the role of RNA modification genes (RMGs) in the diagnosis of OV. Herein, 132 RMGs were retrieved in PubMed, 638 OV and 18 normal ovary samples were retrieved in The Cancer Genome Atlas (TCGA), and GSE18520 cohorts were collected for differential analysis. Finally, PUS7 (Pseudouridine Synthase 7) as differentially expressed RMGs (DEGs-RMGs) was identified as a diagnostic biomarker candidate and evaluated for its specificity and sensitivity using Receiver Operating Characteristic (ROC) analysis in TCGA and GEO data. The protein expression, mutation, protein interaction networks, correlated genes, related pathways, biological processes, cell components, and molecular functions of PUS7 were analyzed as well. The upregulation of PUS7 protein in OV was confirmed by the staining images in HPA and tissue arrays. Collectively, the findings of the present study point towards the potential of PUS7 as a diagnostic marker and therapeutic target for ovarian cancer.", "claims": [{"id": "claim-method", "statement": "The ROC curve was constructed using PUS7 expression profiles in the OV and normal samples by GraphPad Prism 8.0.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34827123", "locator": "sections[11] \"2.9. Statistical Analysis\" paragraph 2", "quote": "The ROC curve was constructed using PUS7 expression profiles in the OV and normal samples by GraphPad Prism 8.0."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Not applicable.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34827123", "locator": "sections[23] \"Institutional Review Board Statement\" paragraph 2", "quote": "Not applicable."}], "state": "complete"}, {"id": "claim-target-result", "statement": "To validate the overexpression of PUS7 in OV rather than normal samples, an Oncomine analysis was performed on ovarian cancer with different pathological types, and found that the PUS7 expression is highly elevated in OV samples with fold change >1 and p < 0.05 (as presented in Figure 3A,B and Table 1).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "To validate the overexpression of PUS7 in OV rather than normal samples, an Oncomine analysis was performed on ovarian cancer with different pathological types, and found that the PUS7 expression is highly elevated in OV samples with fold change >1 and p < 0.05 (as presented in Figure 3A,B and Table 1)."}, "evidence": [{"asset": "source:pmid:34827123", "locator": "sections[14] \"3.2. Expression Validation and Mutation Analysis for PUS7 in Ovarian Cancer\" paragraph 2", "quote": "To validate the overexpression of PUS7 in OV rather than normal samples, an Oncomine analysis was performed on ovarian cancer with different pathological types, and found that the PUS7 expression is highly elevated in OV samples with fold change >1 and p < 0.05 (as presented in Figure 3A,B and Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "To validate the overexpression of PUS7 in OV rather than normal samples, an Oncomine analysis was performed on ovarian cancer with different pathological types, and found that the PUS7 expression is highly elevated in OV samples with fold change >1 and p < 0.05 (as presented in Figure 3A,B and Table 1).", "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:34827123"], "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:GSE119056"], "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:GSE119056"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34827123", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biology10111130", "sha256": "sha256:aee47d50046138b5e7b58f81418d5395dbd71edc7e1670f100ebff3c34a004b5", "bytes": 35420, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biology10111130", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8615213", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE119056", "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=GSE119056", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE119056", "version": null, "note": "Not applicable.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Not applicable.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3357096", "GSM3357097", "GSM3357098", "GSM3357099", "GSM3357100", "GSM3357101", "GSM3357102", "GSM3357103", "GSM3357104", "GSM3357105", "GSM3357106", "GSM3357107", "GSM3357108", "GSM3357109", "GSM3357110", "GSM3357111", "GSM3357112", "GSM3357113"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "21572;19615", "taxon": "synthetic construct; Homo sapiens", "title": "Long noncoding RNA, microRNA, and mRNA expression profiles in ovarian cancer", "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:GSE18520", "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=GSE18520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18520", "version": null, "note": "Not applicable.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Not applicable.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM461348", "GSM461349", "GSM461350", "GSM461351", "GSM461352", "GSM461353", "GSM461354", "GSM461355", "GSM461356", "GSM461357", "GSM461358", "GSM461359", "GSM461360", "GSM461361", "GSM461362", "GSM461363", "GSM461364", "GSM461365", "GSM461366", "GSM461367", "GSM461368", "GSM461369", "GSM461370", "GSM461371", "GSM461372", "GSM461373", "GSM461374", "GSM461375", "GSM461376", "GSM461377", "GSM461378", "GSM461379", "GSM461380", "GSM461381", "GSM461382", "GSM461383", "GSM461384", "GSM461385", "GSM461386", "GSM461387", "GSM461388", "GSM461389", "GSM461390", "GSM461391", "GSM461392", "GSM461393", "GSM461394", "GSM461395", "GSM461396", "GSM461397", "GSM461398", "GSM461399", "GSM461400", "GSM462643", "GSM462644", "GSM462645", "GSM462646", "GSM462647", "GSM462648", "GSM462649", "GSM462650", "GSM462651", "GSM462652"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Whole-genome oligonucleotide expression analysis of papillary serous ovarian adenocarcinomas", "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:GSE119056 not downloaded", "asset:data:geo:GSE119056 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE18520 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Pathway Enrichment"}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-3", "family": null, "specific": null, "label": "Receiver Operating Characteristic (ROC) analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The ROC curve was constructed using PUS7 expression profiles in the OV and normal samples by GraphPad Prism 8.0."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE18520", "GSE119056"], "resolved_accessions": ["GSE18520", "GSE119056"], "statements": ["Not applicable."], "basis": "The paper names GSE18520, GSE119056 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:34827123", "data:geo:GSE119056"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE119056"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:09:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12171, "completion_tokens": 2707, "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:34827123", "type": "paper", "label": "pmid:34827123"}, {"id": "source:pmid:34827123", "type": "manuscript", "label": "PMID 34827123 full text"}, {"id": "data:geo:GSE119056", "type": "dataset", "label": "GEO GSE119056"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34827123", "type": "paper", "label": "pmid:34827123"}, {"id": "source:pmid:34827123", "type": "manuscript", "label": "PMID 34827123 full text"}, {"id": "data:geo:GSE119056", "type": "dataset", "label": "GEO GSE119056"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34827123", "type": "extraction", "used": ["source:pmid:34827123"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE119056", "type": "accession_resolution", "used": ["data:geo:GSE119056"], "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:34827123", "parent_hash": "sha256:1ecdc873234a14983563b845d0b042b89e74c04b566ba643abbd141a69b47554", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE119056 licence not read", "asset:data:geo:GSE119056 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE18520 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["are described in Supplementary Table S2. The immunohistochemistry (IHC) staining intensity was graded from 0 t", "ementary Table S2. The immunohistochemistry (IHC) staining intensity was graded from 0 to 3 ("], "order_basis": "paper_text_order:1851", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Pathway Enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}