Exploring the ceRNA network involving AGAP2-AS1 as a novel biomarker for preeclampsia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39521940", "kind": "science-record", "revision": 4, "content_hash": "sha256:2a91fba7d9728f0aa8b9805f5aa3fba00b301fc1ad7f6b71b64d1e1a411733cb", "created_at": "2026-11-01T20:29:47Z", "updated_at": "2026-11-01T22:55:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the ceRNA network involving AGAP2-AS1 as a novel biomarker for preeclampsia.", "doi": "10.1038/s41598-024-79224-2", "pmid": "39521940", "authors": ["Fan Lu", "Ni Zeng", "Xiang Xiao", "Xingxing Wang", "Han Gong", "Houkang Lei"], "journal": "Scientific reports", "year": 2024, "abstract": "Preeclampsia (PE) is an important research subject in obstetrics. Nevertheless, the underlying mechanisms of PE remain elusive. PE-related expression datasets (GSE96983, GSE96984 and GSE24129) were downloaded from the Gene Expression Omnibus (GEO) database. Firstly, the differentially expressed messenger RNAs (DE-mRNAs), DE-microRNA (DE-miRNAs) and DE-long non-coding RNA (DE-lncRNAs) between PE and control cohorts were identified, and the ceRNA network was constructed. Then candidate hub genes were obtained through five algorithms by the protein-protein intersection (PPI) network of the mRNAs. Further, five hub genes were identified by receiver operating characteristic (ROC) curve and gene expression profiles: DAXX, EFNB1, NCOR2, RBBP4 and SOCS1. The function of 5 hub genes was analyzed and the interaction between drugs and hub genes was predicted. A total of 5 small molecule drugs were predicted, namely benzbromarone, 9,10-phenanthrenequinone, chembl312032, insulin and aldesleukin. AGAP2-AS1 was mainly located in exosome and cytoplasm. Agap2-as1-related regulatory subnetworks were extracted from ceRNA networks which included 41 mRNAs, 2 miRNAs and 1 lncRNA, including the regulated relationship pairs AGAP2-AS1-hsa-miR-497-5p-SRPRB, and AGAP2-AS1-hsa-miR-195-5p-RPL36. In summary, we constructed a competitive endogenous RNA (ceRNA) network to identify five potential biomarkers (DAXX, EFNB1, NCOR2, SOCS1 and RBBP4) of PE. The in-depth analysis of the AGAP2-AS1 regulatory network will help to uncover more important molecules closely related to PE and provide a scientific Reference.", "claims": [{"id": "claim-method", "statement": "Firstly, the gene expression matrix of three PE samples and four control samples in the GSE96984 dataset was analyzed by the voom method in the “limma” R package (version 3.48.3) (|log2FC| > 0.5 and P < 0.05)61, and DE-mRNAs and DE-lncRNAs between the PE groups and the control groups were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39521940", "locator": "sections[13] \"Creation of the competing endogenous RNA (ceRNA) network\" paragraph 2", "quote": "Firstly, the gene expression matrix of three PE samples and four control samples in the GSE96984 dataset was analyzed by the voom method in the “limma” R package (version 3.48.3) (|log2FC| > 0.5 and P < 0.05)61, and DE-mRNAs and DE-lncRNAs between the PE groups and the control groups were identified."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39521940", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified five potential PE biomarkers: DAXX, EFNB1, NCOR2, SOCS1 and RBBP4.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39521940", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In summary, we constructed a competitive endogenous RNA (ceRNA) network to identify five potential biomarkers (DAXX, EFNB1, NCOR2, SOCS1 and RBBP4) of PE."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified five potential PE biomarkers: DAXX, EFNB1, NCOR2, SOCS1 and RBBP4.", "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:39521940"], "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:GSE24129"], "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:GSE24129"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39521940", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-79224-2", "sha256": "sha256:d2657826b1297064365187442f9eb062288e23695a7bc12b3821f5545eabcf8b", "bytes": 41493, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-79224-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11550820", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE24129", "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=GSE24129", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE24129", "version": null, "note": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM594041", "GSM594042", "GSM594043", "GSM594044", "GSM594045", "GSM594046", "GSM594047", "GSM594048", "GSM594049", "GSM594050", "GSM594051", "GSM594052", "GSM594053", "GSM594054", "GSM594055", "GSM594056", "GSM594057", "GSM594058", "GSM594059", "GSM594060", "GSM594061", "GSM594062", "GSM594063", "GSM594064"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling for placentas from pre-eclamptic, unexplained FGR and normal pregnancies.", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE96983", "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=GSE96983", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE96983", "version": null, "note": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2548592", "GSM2548593", "GSM2548594", "GSM2548595", "GSM2548596", "GSM2548597", "GSM2548598"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "20712", "taxon": "Homo sapiens", "title": "Different expression profiles of miRNAs in preeclampsia and normal placenta (miRNA)", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE96984", "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=GSE96984", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE96984", "version": null, "note": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2548599", "GSM2548600", "GSM2548601", "GSM2548602", "GSM2548603", "GSM2548604", "GSM2548605"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "22120", "taxon": "Homo sapiens", "title": "Different expression profiles of lncRNAs, mRNAs and circRNAs in preeclampsia and normal placenta (ceRNA)", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE24129 not downloaded", "asset:data:geo:GSE24129 licence not read", "asset:data:geo:GSE96983 not downloaded", "asset:data:geo:GSE96983 licence not read", "asset:data:geo:GSE96984 not downloaded", "asset:data:geo:GSE96984 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Firstly, the gene expression matrix of three PE samples and four control samples in the GSE96984 dataset was analyzed by the voom method in the “limma” R package (version 3.48.3) (|log2FC| > 0.5 and P < 0.05)61, and DE-mRNAs and DE-lncRNAs between the PE groups and the control groups were identified."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE96983", "GSE96984", "GSE24129"], "resolved_accessions": ["GSE96983", "GSE96984", "GSE24129"], "statements": ["The datasets used and analyzed in the current study are available from the GEO database (https://www.ncbi.nlm.nih.gov/gds) [GSE96983, GSE96984 and GSE24129], StarBase (Http://starbase.sysu.edu.cn), miRTarBase Database (Http://mirtarbase.mbc.nctu.edu.tw), DGIdb database (https://dgidb.org), lncLocator Database (www.csbio.sjtu.edu.cn/bioinf/lncLocator)."], "basis": "The paper names GSE96983, GSE96984, GSE24129 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39521940", "data:geo:GSE24129"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE24129"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:38:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11787, "completion_tokens": 1739, "cached_tokens": 264}}, "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:39521940", "type": "paper", "label": "pmid:39521940"}, {"id": "source:pmid:39521940", "type": "manuscript", "label": "PMID 39521940 full text"}, {"id": "data:geo:GSE24129", "type": "dataset", "label": "GEO GSE24129"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39521940", "type": "paper", "label": "pmid:39521940"}, {"id": "source:pmid:39521940", "type": "manuscript", "label": "PMID 39521940 full text"}, {"id": "data:geo:GSE24129", "type": "dataset", "label": "GEO GSE24129"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39521940", "type": "extraction", "used": ["source:pmid:39521940"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE24129", "type": "accession_resolution", "used": ["data:geo:GSE24129"], "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:39521940", "parent_hash": "sha256:8f1bfc34afb920c30b28b7814a84a1bd2e5bb001ca320488a1bd4a4c2832ced9", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE24129 licence not read", "asset:data:geo:GSE24129 not downloaded", "asset:data:geo:GSE96983 licence not read", "asset:data:geo:GSE96983 not downloaded", "asset:data:geo:GSE96984 licence not read", "asset:data:geo:GSE96984 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative-Polymerase Chain Reaction (RT-qPCR). DAXX, EFNB1, NCOR2, and SOCS1 were highly", "Materials and methods Sample collection and RT-qPCR A total of 8 PE patients and 8 controls at A", "d placenta samples were collected to perform RT-qPCR. This study was approved by Ethics Committee", "perform reverse transcription analysis. The RT-qPCR analysis was performed using the 2xUniversal"], "order_basis": "paper_text_order:1814", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ts (ACOG)2. This study did not involve human in vivo experiments or human transplantation-related"], "order_basis": "paper_text_order:2891", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Firstly, the gene expression matrix of three PE samples and four control samples in the GSE96984 dataset was analyzed by the voom method in the “limma” R package (version 3.48.3) (|log2FC| > 0.5 and P < 0.05)61, and DE-mRNAs and DE-lncRNAs between the PE groups and the control groups were identified."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}