← All .science files
pmid:33028803
ATP6V1G3 Acts as a Key Gene in Recurrent Spontaneous Abortion: An Integrated Bioinformatics Analysis.
Yihong Chen · Jifen Hu
Medical science monitor : international medical journal of experimental and clinical research · 2020 doi:10.12659/MSM.927537
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 2 items
claims array · 1 item
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 10 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 15 items
gaps array · 4 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33028803", "kind": "science-record", "revision": 5, "content_hash": "sha256:2acc2b55166b480c50fc604ab2ac22e41c23d6c029c36bb8def7b1c49d84b451", "created_at": "2026-11-01T15:41:12Z", "updated_at": "2026-11-01T22:02:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ATP6V1G3 Acts as a Key Gene in Recurrent Spontaneous Abortion: An Integrated Bioinformatics Analysis.", "doi": "10.12659/MSM.927537", "pmid": "33028803", "authors": ["Yihong Chen", "Jifen Hu"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2020, "abstract": "BACKGROUND The molecular mechanism of recurrent spontaneous abortion is unclear. It has been suggested that dysregulated genes participate in the pathogenesis of recurrent spontaneous abortion. The aim of this study was to identify the differentially expressed genes (DEGs) and pathways in recurrent spontaneous abortion. MATERIAL AND METHODS Gene expression data series of GSE22490 and GSE26787 were obtained from the GEO database to identify the differentially expressed genes between patients with recurrent miscarriage (Case group) and patients with uncomplicated pregnancies matched for gestational age (Control group). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEEG) were applied to enrich the biological functions and pathways of the identified differentially expressed genes. A protein-protein interaction (PPI) network was constructed thorough the STRING database. Thirty-one cases of recurrent spontaneous abortion (Case group) and 30 cases of artificial abortion (Control group) were included in the study. The protein expression of hub genes in the villi and decidua tissue of the 2 groups was detected by immunohistochemical assay. RESULTS Forty-six DEGs were identified with the enriched biological function mainly in the aspects of glutamate secretion and positive regulation of synapse assembly. KEGG pathway analysis indicated the dysregulated genes were only enriched in the glutamatergic synapse pathway. In the PPI network, 83 nodes and 273 edges with the average node degreed of 6.58 were enriched. The hub gene (ATP6V1G3) of the included 46 genes was identified using Cytohubba software. In the Case group, the high expression of ATP6V1G3 protein was detected in 13 (43.3%) and 10 (33.3%) for placental villus and decidual tissue, respectively. However, the high expression rate in the Control group was 23.3% and 16.7% for placental villus and decidual tissue, respectively. The ATP6V1G3 protein high expression rate was not significantly different between the Case and Control groups (P>0.05). CONCLUSIONS We found differential gene expression profiles in villous and decidual tissues between patients with recurrent miscarriage vs. those with uncomplicated pregnancies. Upregulation of the ATP6V1G3 gene may play an important role in the development of recurrent miscarriage.", "claims": [{"id": "claim-data-access", "statement": "Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33028803", "locator": "sections[3] \"Data series relevant to recurrent abortion\" paragraph 2", "quote": "Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33028803"], "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:GSE22490"], "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:GSE22490"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33028803", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.927537", "sha256": "sha256:4e3a9b48c4d2b6bcd78b85f843c13719e2e84d7544dbc9dfaad22020574e6690", "bytes": 13177, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.927537", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7552882", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22490", "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=GSE22490", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22490", "version": null, "note": "Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM558664", "GSM558665", "GSM558666", "GSM558667", "GSM558668", "GSM558669", "GSM558670", "GSM558671", "GSM558672", "GSM558673"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Increased placental expression and maternal serum levels of apoptosis-inducing TRAIL in recurrent miscarriage", "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:GSE26787", "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=GSE26787", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26787", "version": null, "note": "Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM659103", "GSM659104", "GSM659105", "GSM659106", "GSM659107", "GSM659108", "GSM659109", "GSM659110", "GSM659111", "GSM659112", "GSM659113", "GSM659114", "GSM659115", "GSM659116", "GSM659117"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Comparison of endometrial expression in patients which underwent previous recurrent abortions, implantation failure after IVF/ICSI compared to control fertile", "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:GSE22490 not downloaded", "asset:data:geo:GSE22490 licence not read", "asset:data:geo:GSE26787 not downloaded", "asset:data:geo:GSE26787 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": "protein-protein interaction"}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE22490", "GSE26787"], "resolved_accessions": ["GSE22490", "GSE26787"], "statements": ["Two data series, GSE22490 [13] and GSE26787 [14], relevant to differentially expressed genes between recurrent miscarriage (Case group) and uncomplicated pregnancies matched for gestational age (Control group) were identified."], "basis": "The paper names GSE22490, GSE26787 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33028803", "data:geo:GSE22490"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22490"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:59Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 3, "usage": {"prompt_tokens": 10269, "completion_tokens": 806, "cached_tokens": 784}}, "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:33028803", "type": "paper", "label": "pmid:33028803"}, {"id": "source:pmid:33028803", "type": "manuscript", "label": "PMID 33028803 full text"}, {"id": "data:geo:GSE22490", "type": "dataset", "label": "GEO GSE22490"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33028803", "type": "paper", "label": "pmid:33028803"}, {"id": "source:pmid:33028803", "type": "manuscript", "label": "PMID 33028803 full text"}, {"id": "data:geo:GSE22490", "type": "dataset", "label": "GEO GSE22490"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33028803", "type": "extraction", "used": ["source:pmid:33028803"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22490", "type": "accession_resolution", "used": ["data:geo:GSE22490"], "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:33028803", "parent_hash": "sha256:d33555f808c71d7fc1bcfde42e28223588e6825e7baf42928192742200ff2980", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE22490 licence not read", "asset:data:geo:GSE22490 not downloaded", "asset:data:geo:GSE26787 licence not read", "asset:data:geo:GSE26787 not downloaded", "execution.not_run", "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": 0.93, "evidence": ["cidua tissue of the 2 groups was detected by immunohistochemical assay. RESULTS Forty-six DEGs were identifie"], "order_basis": "paper_text_order:1197", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}