Computer reconstruction of gene networks controlling anxiety levels in humans and laboratory mice.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40144367", "kind": "science-record", "revision": 2, "content_hash": "sha256:d116a428972f21bb9cf6c38a5e3f506ea2e0d4c27c3e23d69d6d82bcdff27712", "created_at": "2026-11-01T20:30:20Z", "updated_at": "2026-11-01T21:34:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Computer reconstruction of gene networks controlling anxiety levels in humans and laboratory mice.", "doi": "10.18699/vjgb-25-19", "pmid": "40144367", "authors": ["E G Vergunov", "V A Savostyanov", "A A Makarova", "E I Nikolaeva", "A N Savostyanov"], "journal": "Vavilovskii zhurnal genetiki i selektsii", "year": 2025, "abstract": "Anxiety is a normotypic human condition, and like any other emotion has an adaptive value. But excessively high or low anxiety has negative consequences for adaptation, which primarily determines the importance of studying these two extreme conditions. At the same time, it is known that the perception of aversive stimuli associated with anxiety leads to changes in the activity of the brain's cingulate cortex. The advantage of animals as models in studying the genetic bases of anxiety in humans is in the ability to subtly control the external conditions of formation of a certain state, the availability of brain tissues, and the ability to create and study transgenic models, including through the use of differentially expressed genes of small laboratory animals from the family Muridae with low and high anxiety. Within the framework of the translational approach, a three-domain potential gene network, which is associated with generalized anxiety in humans, was reconstructed using mouse models with different levels of anxiety by automatically analyzing the texts of scientific articles. One domain is associated with reduced anxiety in humans, the second with increased anxiety, and the third is a dispatcher who activates one of the two domains depending on the status of the organism (genetic, epigenetic, physiological). Stages of work: (I) A list of genes expressed in the cingulate cortex of the wild type CD-1 mouse line from the NCBI GEO database (experiment GSE29014). Using the tools of this database, differences in gene expression levels were revealed in groups of mice with low and high (relatively normal) anxiety. (II) Search for orthologs of DEG in humans and mice associated with anxiety in the OMA Orthology database. (III) Computer reconstruction using the ANDSystem cognitive system based on (a) human orthologous genes from stage (III), (b) human genes from the MalaCards database associated with human anxiety. The proven methods of the translational approach for the reconstruction of gene networks for behavior regulation can be used to identify molecular genetic markers of human personality traits, propensity to psychopathology.", "claims": [{"id": "claim-method", "statement": "Assessing the significance of such a strong overlap using a Bonferroni-corrected hypergeometric distribution for multiple comparisons yields a Padj < 8.4·10–5 (Fig. 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40144367", "locator": "sections[3] \"Results\" paragraph 5", "quote": "Assessing the significance of such a strong overlap using a Bonferroni-corrected hypergeometric distribution for multiple comparisons yields a Padj < 8.4·10–5 (Fig. 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The results of the experiment are presented in the NCBI GEO database with the index GSE29014 (https:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29014).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40144367", "locator": "sections[2] \"Materials and methods\" paragraph 2", "quote": "The results of the experiment are presented in the NCBI GEO database with the index GSE29014 (https:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29014)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reconstructed a three-domain potential human gene network associated with generalized anxiety using mouse models with different anxiety levels and automated analysis of scientific texts.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40144367", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Within the framework of the translational approach, a three-domain potential gene network, which is associated with generalized anxiety in humans, was reconstructed using mouse models with different levels of anxiety by automatically analyzing the texts of scientific articles."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reconstructed a three-domain potential human gene network associated with generalized anxiety using mouse models with different anxiety levels and automated analysis of scientific texts.", "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:40144367"], "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:GSE29014"], "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:GSE29014"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40144367", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18699/vjgb-25-19", "sha256": "sha256:8eaa8b065c9859796ba15fd2793a1c7b8f2f226c793969477d7d3b6eb65ae539", "bytes": 37581, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18699/vjgb-25-19", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11937012", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29014", "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=GSE29014", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29014", "version": null, "note": "The results of the experiment are presented in the NCBI GEO database with the index GSE29014 (https:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29014).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results of the experiment are presented in the NCBI GEO database with the index GSE29014 (https:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29014).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM718824", "GSM718825", "GSM718826", "GSM718827", "GSM718828", "GSM718829", "GSM718830", "GSM718831", "GSM718832", "GSM718833", "GSM718834", "GSM718835", "GSM718836", "GSM718837", "GSM718838", "GSM718839", "GSM718840", "GSM718841", "GSM718842", "GSM718843", "GSM718844", "GSM718845", "GSM718846", "GSM718847", "GSM718848", "GSM718849", "GSM718850", "GSM718851", "GSM718852", "GSM718853", "GSM718854", "GSM718855", "GSM718856", "GSM718857", "GSM718858", "GSM718859", "GSM718860", "GSM718861", "GSM718862", "GSM718863", "GSM718864", "GSM718865", "GSM718866", "GSM718867", "GSM718868", "GSM718869", "GSM718870", "GSM718871", "GSM718872", "GSM718873", "GSM718874", "GSM718875", "GSM718876", "GSM718877", "GSM718878", "GSM718879", "GSM718880", "GSM718881", "GSM718882", "GSM718883", "GSM718884", "GSM718885", "GSM718886", "GSM718887", "GSM718888", "GSM718889", "GSM718890", "GSM718891", "GSM718892", "GSM718893", "GSM718894", "GSM718895", "GSM718896", "GSM718897", "GSM718898", "GSM718899", "GSM718900", "GSM718901"], "sample_count": 78, "group_sizes": null, "group_sizes_basis": null, "platform": "6481", "taxon": "Mus musculus", "title": "Gene expression profiling of high (HAB) vs. low (LAB) and normal (NAB) anxiety-related behavior mice in five laser microdissected brain regions.", "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:GSE29014 not downloaded", "asset:data:geo:GSE29014 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Bonferroni-corrected hypergeometric distribution for multiple comparisons", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Assessing the significance of such a strong overlap using a Bonferroni-corrected hypergeometric distribution for multiple comparisons yields a Padj < 8.4·10–5 (Fig. 1)."}}], "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 (Bonferroni-corrected hypergeometric distribution for multiple comparisons), 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE29014"], "resolved_accessions": ["GSE29014"], "statements": ["The results of the experiment are presented in the NCBI GEO database with the index GSE29014 (https:// www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29014)."], "basis": "The paper names GSE29014 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40144367", "data:geo:GSE29014"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29014"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:49:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 11259, "completion_tokens": 1745, "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:40144367", "type": "paper", "label": "pmid:40144367"}, {"id": "source:pmid:40144367", "type": "manuscript", "label": "PMID 40144367 full text"}, {"id": "data:geo:GSE29014", "type": "dataset", "label": "GEO GSE29014"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40144367", "type": "paper", "label": "pmid:40144367"}, {"id": "source:pmid:40144367", "type": "manuscript", "label": "PMID 40144367 full text"}, {"id": "data:geo:GSE29014", "type": "dataset", "label": "GEO GSE29014"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40144367", "type": "extraction", "used": ["source:pmid:40144367"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29014", "type": "accession_resolution", "used": ["data:geo:GSE29014"], "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:40144367", "parent_hash": "sha256:0e7811ee806740b24e25e41814d5062d4cf0aacf6628b302889989e019af2f15", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE29014 licence not read", "asset:data:geo:GSE29014 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d anxiety in humans, was reconstructed using mouse models with different levels of anxiety by a", "n the cingulate cortex of the wild type CD-1 mouse line from the NCBI GEO database (experiment", "d on the basis of human genes orthologous to mouse genes differentially expressed in the cingul"], "order_basis": "paper_text_order:1046", "id": "assay:1"}]}