Assessment of differentially expressed genes from in vitro matured human oocytes: A bioinformatics approach.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38801311", "kind": "science-record", "revision": 3, "content_hash": "sha256:cebc96e22d7fdcc81aabba95a847d567f0bdd43b2a494778288f09365f6c0da6", "created_at": "2026-11-01T19:20:45Z", "updated_at": "2026-11-01T21:33:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Assessment of differentially expressed genes from in vitro matured human oocytes: A bioinformatics approach.", "doi": "10.5935/1518-0557.20240030", "pmid": "38801311", "authors": ["Gabriel Acácio de Moura", "Mayara Lobato Lourenço", "Yasmim Mendes Rocha", "João Pedro Viana Rodrigues", "Cristian Vicson Pinheiro", "Alice Soares de Queiroz", "Eduardo de Paula Miranda", "Sebastião Evangelista Torquato", "Roberto Nicolete"], "journal": "JBRA assisted reproduction", "year": 2024, "abstract": "OBJECTIVE: One of the techniques that has gained much attention is the in vitro maturation of oocytes for patients who use assisted reproduction techniques. However, its results are still inferior to controlled ovarian stimulation methodologies. Understanding the maturation mechanisms based on analyses can help improve this methodology's results. The work aims to identify the central genes differentially expressed in oocytes after in vitro maturation in the germinal vesicle and metaphase II stages.\nMETHODS: This work is a computational analysis. The entire search will be conducted using the Gene Expression Omnibus (GEO) database. To carry out and obtain the data present in the work, an advanced research search was carried out in the GEO database within the period from January 1, 2013, to January 1, 2023. A total of 27 genomic data were available in the GEO database, of which only two were used.\nRESULTS: Two datasets were identified on the Gene Expression Omnibus database platform: registration data GSE158802 and GSE95477. From the analysis, we identified five downregulated and thirty-six upregulated genes; the central genes that correlated with the main gene proteins found were CLTA and PANK1.\nCONCLUSIONS: There was a differential regulation of gene expression. The most central ones are related to energy capture.", "claims": [{"id": "claim-method", "statement": "The different results were obtained using the online data analysis tool GEO2R (software) to compare gene expression between the groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38801311", "locator": "sections[5] \"Differentially Expressed Genes Screening\" paragraph 2", "quote": "The different results were obtained using the online data analysis tool GEO2R (software) to compare gene expression between the groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This work is a computational analysis; therefore, it is unnecessary to present it to the Ethics and Research Committee with human beings since the data included in the research are available in publicly accessible databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38801311", "locator": "sections[3] \"Type of Study\" paragraph 2", "quote": "This work is a computational analysis; therefore, it is unnecessary to present it to the Ethics and Research Committee with human beings since the data included in the research are available in publicly accessible databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified five downregulated and thirty-six upregulated genes, with CLTA and PANK1 as the central genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38801311", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "From the analysis, we identified five downregulated and thirty-six upregulated genes; the central genes that correlated with the main gene proteins found were CLTA and PANK1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified five downregulated and thirty-six upregulated genes, with CLTA and PANK1 as the central genes.", "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:38801311"], "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:GSE158802"], "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:GSE158802"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38801311", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5935/1518-0557.20240030", "sha256": "sha256:37d96bb37e2928b61f13fa6378dab9ca761012aa0bf477e83a82ab483461d63a", "bytes": 16499, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.5935/1518-0557.20240030", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11349261", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE158802", "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=GSE158802", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE158802", "version": null, "note": "This work is a computational analysis; therefore, it is unnecessary to present it to the Ethics and Research Committee with human beings since the data included in the research are available in publicly accessible databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This work is a computational analysis; therefore, it is unnecessary to present it to the Ethics and Research Committee with human beings since the data included in the research are available in publicly accessible databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4810612", "GSM4810613", "GSM4810614", "GSM4810615", "GSM4810616", "GSM4810617", "GSM4810618", "GSM4810619", "GSM4810620", "GSM4810621", "GSM4810622", "GSM4810623", "GSM4810624", "GSM4810625", "GSM4810626", "GSM4810627", "GSM4810628", "GSM4810629", "GSM4810630", "GSM4810631", "GSM4810632", "GSM4810633", "GSM4810634", "GSM4810635", "GSM4810636", "GSM4810637", "GSM4810638", "GSM4810639", "GSM4810640", "GSM4810641", "GSM4810642", "GSM4810643", "GSM4810644", "GSM4810645", "GSM4810646", "GSM4810647", "GSM4810648", "GSM4810649", "GSM4810650", "GSM4810651", "GSM4810652", "GSM4810653", "GSM4810654", "GSM4810655", "GSM4810656", "GSM4810657", "GSM4810658", "GSM4810659", "GSM4810660", "GSM4810661", "GSM4810662", "GSM4810663", "GSM4810664", "GSM4810665", "GSM4810666", "GSM4810667", "GSM4810668", "GSM4810669", "GSM4810670", "GSM4810671", "GSM4810672", "GSM4810673", "GSM4810674", "GSM4810675", "GSM4810676", "GSM4810677", "GSM4810678", "GSM4810679", "GSM4810680", "GSM4810681", "GSM4810682", "GSM4810683", "GSM4810684", "GSM4810685", "GSM4810686"], "sample_count": 75, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Impact of maternal age and in vitro maturation on the transcriptome of denuded human oocytes", "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:GSE95477", "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=GSE95477", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95477", "version": null, "note": "This work is a computational analysis; therefore, it is unnecessary to present it to the Ethics and Research Committee with human beings since the data included in the research are available in publicly accessible databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This work is a computational analysis; therefore, it is unnecessary to present it to the Ethics and Research Committee with human beings since the data included in the research are available in publicly accessible databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2514771", "GSM2514772", "GSM2514773", "GSM2514774", "GSM2514775", "GSM2514776", "GSM2514777", "GSM2514778", "GSM2514779", "GSM2514780", "GSM2514781", "GSM2514782", "GSM2514783", "GSM2514784", "GSM2514785", "GSM2514786", "GSM2514787", "GSM2514788", "GSM2514789", "GSM2514790"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Transcriptome analysis of immature and matured human oocytes from patients of young and advanced maternal age", "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:GSE158802 not downloaded", "asset:data:geo:GSE158802 licence not read", "asset:data:geo:GSE95477 not downloaded", "asset:data:geo:GSE95477 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "GEO2R differential gene-expression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The different results were obtained using the online data analysis tool GEO2R (software) to compare gene expression between the groups."}}], "targets": [], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (GEO2R differential gene-expression analysis), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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