Gene expression analysis of Schizophrenia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40162448", "kind": "science-record", "revision": 2, "content_hash": "sha256:d91df271a0c696258ed55e882bfbeef874b3ed77d9a9c6f26b15ce6468b113cf", "created_at": "2026-11-01T20:30:21Z", "updated_at": "2026-11-01T21:34:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression analysis of Schizophrenia.", "doi": "10.6026/9732063002001441", "pmid": "40162448", "authors": ["Gunjan Sharma", "Ansh Malik", "Satyendra Tripathi", "Vishwajit Deshmukh", "Ashlesh Patil"], "journal": "Bioinformation", "year": 2024, "abstract": "Schizophrenia is a chronic psychiatric disorder marked by cognitive deficits associated with prefrontal cortical dysfunction, particularly in Broadmann Area 10 (BA 10), where gray matter reduction is observed. The genetic mechanisms behind these abnormalities remain unclear. Therefore, it is of interest to analyze altered gene expression and pathways in the prefrontal cortex of schizophrenia patients. We used two GEO datasets - GSE12654 (discovery) and GSE17612 (validation) and differential gene expression was assessed between schizophrenia patients and healthy controls. Validation confirmed three upregulated genes (S100A9, S100A8, BCL2A1) and one downregulated gene (CBLB), with protein interaction analysis revealing that upregulated genes were linked to immune and apoptotic processes, while downregulated genes suppressed EGF pathways. These findings suggest immune dysfunction and gray matter loss in schizophrenia, highlighting potential biomarkers and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Gene expression profiles were compared between schizophrenia patients and age-matched healthy controls using an unpaired t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40162448", "locator": "sections[5] \"Data analysis:\" paragraph 2", "quote": "Gene expression profiles were compared between schizophrenia patients and age-matched healthy controls using an unpaired t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40162448", "locator": "sections[3] \"Data selection and characteristics of discovery and validation datasets:\" paragraph 2", "quote": "The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Validation confirmed three upregulated genes (S100A9, S100A8, BCL2A1) and one downregulated gene (CBLB), with protein interaction analysis revealing that upregulated genes were linked to immune and apoptotic processes, while downregulated genes suppressed EGF pathways.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40162448", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Validation confirmed three upregulated genes (S100A9, S100A8, BCL2A1) and one downregulated gene (CBLB), with protein interaction analysis revealing that upregulated genes were linked to immune and apoptotic processes, while downregulated genes suppressed EGF pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Validation confirmed three upregulated genes (S100A9, S100A8, BCL2A1) and one downregulated gene (CBLB), with protein interaction analysis revealing that upregulated genes were linked to immune and apoptotic processes, while downregulated genes suppressed EGF pathways.", "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:40162448"], "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:GSE12654"], "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:GSE12654"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40162448", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.6026/9732063002001441", "sha256": "sha256:86336ce6f569649d9984f0938d0778e1df7f3adc7b7668696171c90e09897856", "bytes": 24630, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.6026/9732063002001441", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11953522", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12654", "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=GSE12654", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12654", "version": null, "note": "The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM317649", "GSM317650", "GSM317651", "GSM317652", "GSM317653", "GSM317654", "GSM317655", "GSM317656", "GSM317657", "GSM317658", "GSM317659", "GSM317660", "GSM317661", "GSM317662", "GSM317663", "GSM317664", "GSM317665", "GSM317666", "GSM317667", "GSM317668", "GSM317669", "GSM317670", "GSM317671", "GSM317672", "GSM317673", "GSM317674", "GSM317675", "GSM317676", "GSM317677", "GSM317678", "GSM317679", "GSM317680", "GSM317681", "GSM317682", "GSM317683", "GSM317684", "GSM317685", "GSM317686", "GSM317687", "GSM317688", "GSM317689", "GSM317690", "GSM317691", "GSM317692", "GSM317693", "GSM317694", "GSM317695", "GSM317696", "GSM317697", "GSM317698"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "8300", "taxon": "Homo sapiens", "title": "Gene expression from human prefrontal cortex (BA10)", "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:GSE17612", "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=GSE17612", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17612", "version": null, "note": "The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM439778", "GSM439779", "GSM439780", "GSM439781", "GSM439782", "GSM439783", "GSM439784", "GSM439785", "GSM439786", "GSM439787", "GSM439788", "GSM439789", "GSM439790", "GSM439791", "GSM439792", "GSM439793", "GSM439794", "GSM439795", "GSM439796", "GSM439797", "GSM439798", "GSM439799", "GSM439800", "GSM439801", "GSM439802", "GSM439803", "GSM439804", "GSM439805", "GSM439806", "GSM439807", "GSM439808", "GSM439809", "GSM439810", "GSM439811", "GSM439812", "GSM439813", "GSM439814", "GSM439815", "GSM439816", "GSM439817", "GSM439818", "GSM439819", "GSM439820", "GSM439821", "GSM439822", "GSM439823", "GSM439824", "GSM439825", "GSM439826", "GSM439827", "GSM439828"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Comparison of post-mortem tissue from brain BA10 region between schizophrenic and control patients.", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE12654 not downloaded", "asset:data:geo:GSE12654 licence not read", "asset:data:geo:GSE17612 not downloaded", "asset:data:geo:GSE17612 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "kmeans", "label": "Clustering", "dsl_operations": ["kmeans_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "k-means"}}, {"id": "method-2", "family": null, "specific": null, "label": "unpaired t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Gene expression profiles were compared between schizophrenia patients and age-matched healthy controls using an unpaired t-test."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["kmeans_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kmeans."}, "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": ["GSE12654", "GSE17612"], "resolved_accessions": ["GSE12654", "GSE17612"], "statements": ["The first dataset, GSE12654, served as the discovery dataset and included samples from 13 schizophrenia patients (age 44 ± 14 years, 5 females) and 15 age-matched healthy controls (age 48 ± 11 years, 6 females)."], "basis": "The paper names GSE12654, GSE17612 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["kmeans_fit"], "assets": ["source:pmid:40162448", "data:geo:GSE12654"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12654"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:49:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7609, "completion_tokens": 1203, "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:40162448", "type": "paper", "label": "pmid:40162448"}, {"id": "source:pmid:40162448", "type": "manuscript", "label": "PMID 40162448 full text"}, {"id": "data:geo:GSE12654", "type": "dataset", "label": "GEO GSE12654"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40162448", "type": "paper", "label": "pmid:40162448"}, {"id": "source:pmid:40162448", "type": "manuscript", "label": "PMID 40162448 full text"}, {"id": "data:geo:GSE12654", "type": "dataset", "label": "GEO GSE12654"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40162448", "type": "extraction", "used": ["source:pmid:40162448"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12654", "type": "accession_resolution", "used": ["data:geo:GSE12654"], "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:40162448", "parent_hash": "sha256:5bb48606932ddbb20ef50ed68c7dcfc1e3a70ac92dc9ae93caf6e711d74e12b9", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE12654 licence not read", "asset:data:geo:GSE12654 not downloaded", "asset:data:geo:GSE17612 licence not read", "asset:data:geo:GSE17612 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["2). The red cluster was associated with the apoptosis network, specifically involving the Bcl-2 fa", "the EGF receptor signalling pathway and the apoptosis signalling pathway, were identified, providi", "ificant genes with k means clustering → Red: apoptosis network (Bcl-2 family protein complex), yell", "the EGF receptor signalling pathway and the apoptosis signalling pathway. Source: PANTHER Classifi"], "order_basis": "paper_text_order:1263", "id": "assay:1"}, {"role": "analysis", "definition_id": "clustering", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["kmeans_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["k-means"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}