Integrated bioinformatics analysis elucidates granulosa cell whole-transcriptome landscape of PCOS in China.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37537636", "kind": "science-record", "revision": 5, "content_hash": "sha256:34010bc75721bed76a4e38337840f363c27de928e88c4b6df02ddd100de3a5a2", "created_at": "2026-11-01T19:02:18Z", "updated_at": "2026-11-01T22:52:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis elucidates granulosa cell whole-transcriptome landscape of PCOS in China.", "doi": "10.1186/s13048-023-01223-0", "pmid": "37537636", "authors": ["Qingfang Li", "Yimiao Sang", "Qingqing Chen", "Bingru Ye", "Xiaoqian Zhou", "Yimin Zhu"], "journal": "Journal of ovarian research", "year": 2023, "abstract": "BACKGROUND: Polycystic ovary syndrome (PCOS) is a common reproductive, neuroendocrine, and metabolic disorder in women of reproductive age that affects up to 5-10% of women of reproductive age. The aetiology of follicle development arrest and critical issues regarding the abnormal follicular development in PCOS remain unclear. The present study aims to systematically evaluate granulosa cell whole-transcriptome sequencing data to gain more insights into the transcriptomic landscape and molecular mechanism of PCOS in China.\nMETHODS: In the present study, the microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, and GSE145296 were downloaded from the Gene Expression Omnibus (GEO) database. Subsequently, differential expression analysis was performed on the PCOS and control groups, followed by functional interaction prediction analysis to investigate gene-regulatory circuits in PCOS. Finally, hub genes and their associated ncRNAs were validated by qPCR in human-luteinized granulosa (hGL) cells and were correlated with the clinical characteristics of the patients.\nRESULTS: A total of 200 differentially expressed mRNAs, 3 differentially expressed miRNAs, 52 differentially expressed lncRNAs, and 66 differentially expressed circRNAs were found in PCOS samples compared with controls. GO and KEGG enrichment analyses indicated that the DEGs were mostly enriched in phospholipid metabolic processes, steroid biosynthesis and inflammation related pathways. In addition, the upregulated miRNA hsa-miR-205-5p was significantly enriched in the ceRNA network, and two hub genes, MVD and PNPLA3, were regulated by hsa-miR-205-5p, which means that hsa-miR-205-5p may play a fundamental role in the pathogenesis of PCOS. We also found that MVD and PNPLA3 were related to metabolic processes and ovarian steroidogenesis, which may be the cause of the follicle development arrest in PCOS patients.\nCONCLUSIONS: In summary, we systematically constructed a ceRNA network depicting the interactions between the ncRNAs and the hub genes in PCOS and control subjects and correlated the hub genes with the clinical characteristics of the patients, which provides valuable insights into the granulosa cell whole-transcriptome landscape of PCOS in China.", "claims": [{"id": "claim-method", "statement": "Differential gene analysis was performed by edgeR and the limma package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37537636", "locator": "sections[4] \"Identification of differentially expressed mRNAs and noncoding RNAs\" paragraph 2", "quote": "Differential gene analysis was performed by edgeR and the limma package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37537636", "locator": "sections[27] \"notes\" paragraph 1", "quote": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 200 differentially expressed mRNAs, 3 differentially expressed miRNAs, 52 differentially expressed lncRNAs, and 66 differentially expressed circRNAs were found in PCOS samples compared with controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37537636", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 200 differentially expressed mRNAs, 3 differentially expressed miRNAs, 52 differentially expressed lncRNAs, and 66 differentially expressed circRNAs were found in PCOS samples compared with controls."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 200 differentially expressed mRNAs, 3 differentially expressed miRNAs, 52 differentially expressed lncRNAs, and 66 differentially expressed circRNAs were found in PCOS samples compared with controls.", "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:37537636"], "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:GSE138518"], "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:GSE138518"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37537636", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13048-023-01223-0", "sha256": "sha256:5bb40c42115e1bf6aae74eee1ede1daea885912f29db7a8b523a09889b713cca", "bytes": 39703, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13048-023-01223-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10398987", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE138518", "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=GSE138518", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138518", "version": null, "note": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4110156", "GSM4110157", "GSM4110158", "GSM4110159", "GSM4110160", "GSM4110161"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Transcriptome Profiling Reveals the key genes and pathways involved in polycystic ovary syndrome [RNA-seq]", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE138572", "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=GSE138572", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138572", "version": null, "note": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4113831", "GSM4113832", "GSM4113833", "GSM4113834", "GSM4113835", "GSM4113836", "GSM4113837", "GSM4113838", "GSM4113839", "GSM4113840"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Identification of microRNAs involved in polycystic ovary syndrome based on High-throughput sequencing [miRNA-seq]", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE145296", "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=GSE145296", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE145296", "version": null, "note": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4314377", "GSM4314378", "GSM4314379", "GSM4314380", "GSM4314381", "GSM4314382", "GSM4314383", "GSM4314384", "GSM4314385", "GSM4314386", "GSM4314387", "GSM4314388"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "28148", "taxon": "Homo sapiens", "title": "Expression profiling of circular RNA in the cumulus cells of patients with polycystic ovary syndrome", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE168404", "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=GSE168404", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE168404", "version": null, "note": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5138269", "GSM5138270", "GSM5138271", "GSM5138272", "GSM5138273", "GSM5138274", "GSM5138275", "GSM5138276", "GSM5138277", "GSM5138278", "GSM5138279", "GSM5138280", "GSM5138281", "GSM5138282", "GSM5138283", "GSM5138284", "GSM5138285", "GSM5138286", "GSM5138287", "GSM5138288", "GSM5138289", "GSM5138290", "GSM5138291", "GSM5138292", "GSM5138293", "GSM5138294", "GSM5138295", "GSM5138296", "GSM5138297", "GSM5138298", "GSM5138299", "GSM5138300", "GSM5138301", "GSM5138302", "GSM5138303", "GSM5138304", "GSM5138305", "GSM5138306", "GSM5138307", "GSM5138308"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Multiomics analysis reveals molecular abnormalities in granulosa cells of women with polycystic ovary syndrome", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE193123", "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=GSE193123", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE193123", "version": null, "note": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5773736", "GSM5773737", "GSM5773738", "GSM5773739", "GSM5773740", "GSM5773741"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Effects of androgen excess-related metabolic disturbances on granulosa cell function and follicular development", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE95728", "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=GSE95728", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95728", "version": null, "note": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2522774", "GSM2522775", "GSM2522776", "GSM2522777", "GSM2522778", "GSM2522779", "GSM2522780", "GSM2522781", "GSM2522782", "GSM2522783", "GSM2522784", "GSM2522785", "GSM2522786", "GSM2522787"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "Long noncoding RNA expression profiles in granulosa cells from PCOS patients and women with normal ovarian reserve", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE138518 not downloaded", "asset:data:geo:GSE138518 licence not read", "asset:data:geo:GSE138572 not downloaded", "asset:data:geo:GSE138572 licence not read", "asset:data:geo:GSE145296 not downloaded", "asset:data:geo:GSE145296 licence not read", "asset:data:geo:GSE168404 not downloaded", "asset:data:geo:GSE168404 licence not read", "asset:data:geo:GSE193123 not downloaded", "asset:data:geo:GSE193123 licence not read", "asset:data:geo:GSE95728 not downloaded", "asset:data:geo:GSE95728 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "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": "Differential gene analysis was performed by edgeR and the limma package."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "limma"}}], "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: edger."}, "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": ["GSE138518", "GSE168404", "GSE193123", "GSE138572", "GSE95728", "GSE145296"], "resolved_accessions": ["GSE138518", "GSE168404", "GSE193123", "GSE138572", "GSE95728", "GSE145296"], "statements": ["The microarray datasets GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 were downloaded from GEO database (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE138518, GSE168404, GSE193123, GSE138572, GSE95728, GSE145296 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37537636", "data:geo:GSE138518"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE138518"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:48:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11608, "completion_tokens": 2181, "cached_tokens": 256}}, "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:37537636", "type": "paper", "label": "pmid:37537636"}, {"id": "source:pmid:37537636", "type": "manuscript", "label": "PMID 37537636 full text"}, {"id": "data:geo:GSE138518", "type": "dataset", "label": "GEO GSE138518"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37537636", "type": "paper", "label": "pmid:37537636"}, {"id": "source:pmid:37537636", "type": "manuscript", "label": "PMID 37537636 full text"}, {"id": "data:geo:GSE138518", "type": "dataset", "label": "GEO GSE138518"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37537636", "type": "extraction", "used": ["source:pmid:37537636"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE138518", "type": "accession_resolution", "used": ["data:geo:GSE138518"], "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:37537636", "parent_hash": "sha256:8a9a0f45e99c42b982141f938d4966051f984fedb0f159f2ae8f07c03b81b3d0", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE138518 licence not read", "asset:data:geo:GSE138518 not downloaded", "asset:data:geo:GSE138572 licence not read", "asset:data:geo:GSE138572 not downloaded", "asset:data:geo:GSE145296 licence not read", "asset:data:geo:GSE145296 not downloaded", "asset:data:geo:GSE168404 licence not read", "asset:data:geo:GSE168404 not downloaded", "asset:data:geo:GSE193123 licence not read", "asset:data:geo:GSE193123 not downloaded", "asset:data:geo:GSE95728 licence not read", "asset:data:geo:GSE95728 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["in China. METHODS: In the present study, the microarray datasets GSE138518, GSE168404, GSE193123, GS"], "order_basis": "paper_text_order:627", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["nd their associated ncRNAs were validated by qPCR in human-luteinized granulosa (hGL) cells an"], "order_basis": "paper_text_order:1042", "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": 0.77, "evidence": ["All the cell models used in this study were cultured in a humidified atmosphere of 5% CO2 and 95% ai"], "order_basis": "paper_text_order:2608", "id": "assay:3"}, {"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": ["Differential gene analysis was performed by edgeR and the limma package."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}