Coexpression Network Analysis of Benign and Malignant Phenotypes of SIV-Infected Sooty Mangabey and Rhesus Macaque.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27280726", "kind": "science-record", "revision": 4, "content_hash": "sha256:cb4c265cbe1412cd9eba45ef0d17390b2f64c02a2bcb8d42afda7a62ab87c090", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:20:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Coexpression Network Analysis of Benign and Malignant Phenotypes of SIV-Infected Sooty Mangabey and Rhesus Macaque.", "doi": "10.1371/journal.pone.0156170", "pmid": "27280726", "authors": ["Zhao-Wan Yang", "Yan-Hua Jiang", "Chuang Ma", "Guido Silvestri", "Steven E Bosinger", "Bai-Lian Li", "Ambrose Jong", "Yan-Hong Zhou", "Sheng-He Huang"], "journal": "PloS one", "year": 2016, "abstract": "To explore the differences between the extreme SIV infection phenotypes, nonprogression (BEN: benign) to AIDS in sooty mangabeys (SMs) and progression to AIDS (MAL: malignant) in rhesus macaques (RMs), we performed an integrated dual positive-negative connectivity (DPNC) analysis of gene coexpression networks (GCN) based on publicly available big data sets in the GEO database of NCBI. The microarray-based gene expression data sets were generated, respectively, from the peripheral blood of SMs and RMs at several time points of SIV infection. Significant differences of GCN changes in DPNC values were observed in SIV-infected SMs and RMs. There are three groups of enriched genes or pathways (EGPs) that are associated with three SIV infection phenotypes (BEN+, MAL+ and mixed BEN+/MAL+). The MAL+ phenotype in SIV-infected RMs is specifically associated with eight EGPs, including the protein ubiquitin proteasome system, p53, granzyme A, gramzyme B, polo-like kinase, Glucocorticoid receptor, oxidative phosyphorylation and mitochondrial signaling. Mitochondrial (endosymbiotic) dysfunction is solely present in RMs. Specific BEN+ pattern changes in four EGPs are identified in SIV-infected SMs, including the pathways contributing to interferon signaling, BRCA1/DNA damage response, PKR/INF induction and LGALS8. There are three enriched pathways (PRR-activated IRF signaling, RIG1-like receptor and PRR pathway) contributing to the mixed (BEN+/MAL+) phenotypes of SIV infections in RMs and SMs, suggesting that these pathways play a dual role in the host defense against viral infections. Further analysis of Hub genes in these GCNs revealed that the genes LGALS8 and IL-17RA, which positively regulate the barrier function of the gut mucosa and the immune homeostasis with the gut microbiota (exosymbiosis), were significantly differentially expressed in RMs and SMs. Our data suggest that there exists an exo- (dysbiosis of the gut microbiota) and endo- (mitochondrial dysfunction) symbiotic imbalance (EESI) in HIV/SIV infections. Dissecting the mechanisms of the exo-endo symbiotic balance (EESB) that maintains immune homeostasis and the EESI problems in HIV/SIV infections may lead to a better understanding of the pathogenesis of AIDS and the development of novel interventions for the rational control of this disease.", "claims": [{"id": "claim-method", "statement": "The gene coexpression networks (GCNs) were respectively reconstructed for SM and RM at different time points of SIV infection.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27280726", "locator": "sections[17] \"Network reconstruction\" paragraph 2", "quote": "The gene coexpression networks (GCNs) were respectively reconstructed for SM and RM at different time points of SIV infection."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression values can be obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/, accession number GSE16147).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27280726", "locator": "sections[13] \"Microarray Dataset\" paragraph 3", "quote": "The expression values can be obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/, accession number GSE16147)."}], "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:27280726"], "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:GSE16147"], "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:GSE16147"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27280726", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0156170", "sha256": "sha256:9d4095b1f861cbc73c0674763ac2b006610684eaf26cbc70e10bd9fdacc25f92", "bytes": 47003, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0156170", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4900581", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16147", "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=GSE16147", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16147", "version": null, "note": "The expression values can be obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/, accession number GSE16147).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The expression values can be obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/, accession number GSE16147).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM404478", "GSM404479", "GSM404480", "GSM404481", "GSM404482", "GSM404483", "GSM404484", "GSM404485", "GSM404486", "GSM404487", "GSM404488", "GSM404489", "GSM404490", "GSM404491", "GSM404492", "GSM404493", "GSM404494", "GSM404495", "GSM404496", "GSM404497", "GSM404498", "GSM404499", "GSM404500", "GSM404501", "GSM404502", "GSM404503", "GSM404504", "GSM404505", "GSM404506", "GSM404507", "GSM404508", "GSM404509", "GSM404510", "GSM404511", "GSM404512", "GSM404513", "GSM404514", "GSM404515", "GSM404516", "GSM404517", "GSM404518", "GSM404519", "GSM404520", "GSM404521", "GSM404522", "GSM404523", "GSM404524", "GSM404525", "GSM404526", "GSM404527", "GSM404528", "GSM404529", "GSM404530", "GSM404531", "GSM404532", "GSM404533", "GSM404534", "GSM404535", "GSM404536", "GSM404537", "GSM404538", "GSM404539", "GSM404540", "GSM404541", "GSM404542", "GSM404543", "GSM404544", "GSM404545", "GSM404546", "GSM404547", "GSM404548", "GSM404549", "GSM404550", "GSM404551", "GSM404552", "GSM404553", "GSM404554", "GSM404555", "GSM404556", "GSM404557", "GSM404558", "GSM404559", "GSM404560", "GSM404561", "GSM404562", "GSM404563", "GSM404564", "GSM404565", "GSM404566", "GSM404567", "GSM404568", "GSM404569", "GSM404570", "GSM404571"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "3535", "taxon": "Macaca mulatta; Cercocebus atys", "title": "Microarray Expression Analysis of SIV infection of Sooty Mangabeys", "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:GSE16147 not downloaded", "asset:data:geo:GSE16147 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The gene coexpression networks (GCNs) were respectively reconstructed for SM and RM at different time points of SIV infection."}}], "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE16147"], "resolved_accessions": ["GSE16147"], "statements": ["The expression values can be obtained from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/, accession number GSE16147)."], "basis": "The paper names GSE16147 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pearson_r"], "assets": ["source:pmid:27280726", "data:geo:GSE16147"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16147"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 0, "usage": {}}, "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:27280726", "type": "paper", "label": "pmid:27280726"}, {"id": "source:pmid:27280726", "type": "manuscript", "label": "PMID 27280726 full text"}, {"id": "data:geo:GSE16147", "type": "dataset", "label": "GEO GSE16147"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27280726", "type": "paper", "label": "pmid:27280726"}, {"id": "source:pmid:27280726", "type": "manuscript", "label": "PMID 27280726 full text"}, {"id": "data:geo:GSE16147", "type": "dataset", "label": "GEO GSE16147"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27280726", "type": "extraction", "used": ["source:pmid:27280726"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16147", "type": "accession_resolution", "used": ["data:geo:GSE16147"], "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:27280726", "parent_hash": "sha256:4eadaa7fa8600c0ee73cfb39e5815d79b43d98ca90ea39464b3feb3da70547dd", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE16147 licence not read", "asset:data:geo:GSE16147 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": ["g data sets in the GEO database of NCBI. The microarray-based gene expression data sets were generat"], "order_basis": "paper_text_order:463", "id": "assay:1"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The gene coexpression networks (GCNs) were respectively reconstructed for SM and RM at different time points of SIV infection."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}