Monocyte-related gene biomarkers for latent and active tuberculosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34751089", "kind": "science-record", "revision": 5, "content_hash": "sha256:f531257e153f2f0a50ec027f307ced6920dc92ff15448702fa81df50b824e3bf", "created_at": "2026-11-01T17:36:26Z", "updated_at": "2026-11-01T22:47:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Monocyte-related gene biomarkers for latent and active tuberculosis.", "doi": "10.1080/21655979.2021.2003931", "pmid": "34751089", "authors": ["Yu Li", "Yaju Deng", "Jie He"], "journal": "Bioengineered", "year": 2021, "abstract": "Monocytes are closely associated with tuberculosis (TB). Latent tuberculosis in some patients gradually develops into its active state. This study aimed to investigate the role of hub monocyte-associated genes in distinguishing latent TB infection (LTBI) from active TB. The gene expression profiles of 15 peripheral blood mononuclear cells (PBMCs) samples were downloaded from the gene expression omnibus (GEO) database, GSE54992. The monocyte abundance was high in active TB as evaluated by the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm. The limma test and correlation analysis documented 165 differentially expressed monocyte-related genes (DEMonRGs) between latent TB and active TB. Functional annotation and enrichment analyses of the DEMonRGs using the database for annotation, visualization, and integration discovery (DAVID) tools showed enrichment of inflammatory response mechanisms and immune-related pathways. A protein-protein interaction network was constructed with a node degree ≥10. The expression levels of these hub DEMonRGs (SERPINA1, FUCA2, and HP) were evaluated and verified using several independent datasets and clinical settings. Finally, a single sample scoring method was used to establish a gene signature for the three DEMonRGs, distinguishing active TB from latent TB. The findings of the present study provide a better understanding of monocyte-related molecular fundamentals in TB progression and contribute to the identification of new potential biomarkers for the diagnosis of active TB.", "claims": [{"id": "claim-method", "statement": "The ‘limma’ package in the R software was used to identify the DEGs among latent and active TB samples. If |fold change|≥1 and P < 0.05, genes were considered to be differentially expressed. Finally, Pearson’s correlation analysis was used to identify genes related to monocyte abundance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34751089", "locator": "sections[5] \"Screening monocyte-related genes\" paragraph 2", "quote": "The ‘limma’ package in the R software was used to identify the DEGs among latent and active TB samples. If |fold change|≥1 and P < 0.05, genes were considered to be differentially expressed. Finally, Pearson’s correlation analysis was used to identify genes related to monocyte abundance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34751089", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among the PBMCs of patients with latent and active tuberculosis, 165 DEMonRGs were obtained through the ‘limma’ test and correlation analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34751089", "locator": "sections[15] \"Results\" paragraph 2", "quote": "Among the PBMCs of patients with latent and active tuberculosis, 165 DEMonRGs were obtained through the ‘limma’ test and correlation analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Among the PBMCs of patients with latent and active tuberculosis, 165 DEMonRGs were obtained through the ‘limma’ test and correlation analysis.", "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:34751089"], "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:GSE19444"], "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:GSE19444"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34751089", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/21655979.2021.2003931", "sha256": "sha256:8c6605aa032dc3fdc67af86a3c0ec8306fd1c031a50c15f11d0b4a36996b1201", "bytes": 36380, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/21655979.2021.2003931", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8809927", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19444", "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=GSE19444", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19444", "version": null, "note": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM484595", "GSM484596", "GSM484597", "GSM484598", "GSM484599", "GSM484600", "GSM484601", "GSM484602", "GSM484603", "GSM484604", "GSM484605", "GSM484606", "GSM484607", "GSM484608", "GSM484609", "GSM484610", "GSM484611", "GSM484612", "GSM484613", "GSM484614", "GSM484615", "GSM484616", "GSM484617", "GSM484618", "GSM484619", "GSM484620", "GSM484621", "GSM484622", "GSM484623", "GSM484624", "GSM484625", "GSM484626", "GSM484627", "GSM484628", "GSM484629", "GSM484630", "GSM484631", "GSM484632", "GSM484633", "GSM484634", "GSM484635", "GSM484636", "GSM484637", "GSM484638", "GSM484639", "GSM484640", "GSM484641", "GSM484642", "GSM484643", "GSM484644", "GSM484645", "GSM484646", "GSM484647", "GSM484648"], "sample_count": 54, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Blood Transcriptional Profiles of Active and Latent TB (UK Test Set)", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37250", "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=GSE37250", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37250", "version": null, "note": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM914353", "GSM914354", "GSM914355", "GSM914356", "GSM914357", "GSM914358", "GSM914359", "GSM914360", "GSM914361", "GSM914362", "GSM914363", "GSM914364", "GSM914365", "GSM914366", "GSM914367", "GSM914368", "GSM914369", "GSM914370", "GSM914371", "GSM914372", "GSM914373", "GSM914374", "GSM914375", "GSM914376", "GSM914377", "GSM914378", "GSM914379", "GSM914380", "GSM914381", "GSM914382", "GSM914383", "GSM914384", "GSM914385", "GSM914386", "GSM914387", "GSM914388", "GSM914389", "GSM914390", "GSM914391", "GSM914392", "GSM914393", "GSM914394", "GSM914395", "GSM914396", "GSM914397", "GSM914398", "GSM914399", "GSM914400", "GSM914401", "GSM914402", "GSM914403", "GSM914404", "GSM914405", "GSM914406", "GSM914407", "GSM914408", "GSM914409", "GSM914410", "GSM914411", "GSM914412", "GSM914413", "GSM914414", "GSM914415", "GSM914416", "GSM914417", "GSM914418", "GSM914419", "GSM914420", "GSM914421", "GSM914422", "GSM914423", "GSM914424", "GSM914425", "GSM914426", "GSM914427", "GSM914428", "GSM914429", "GSM914430", "GSM914431", "GSM914432", "GSM914433", "GSM914434", "GSM914435", "GSM914436", "GSM914437", "GSM914438", "GSM914439", "GSM914440", "GSM914441", "GSM914442", "GSM914443", "GSM914444", "GSM914445", "GSM914446", "GSM914447", "GSM914448", "GSM914449", "GSM914450", "GSM914451", "GSM914452", "GSM914453", "GSM914454", "GSM914455", "GSM914456", "GSM914457", "GSM914458", "GSM914459", "GSM914460", "GSM914461", "GSM914462", "GSM914463", "GSM914464", "GSM914465", "GSM914466", "GSM914467", "GSM914468", "GSM914469", "GSM914470", "GSM914471", "GSM914472", "GSM914473", "GSM914474", "GSM914475", "GSM914476", "GSM914477", "GSM914478", "GSM914479", "GSM914480", "GSM914481", "GSM914482", "GSM914483", "GSM914484", "GSM914485", "GSM914486", "GSM914487", "GSM914488", "GSM914489", "GSM914490", "GSM914491", "GSM914492", "GSM914493", "GSM914494", "GSM914495", "GSM914496", "GSM914497", "GSM914498", "GSM914499", "GSM914500", "GSM914501", "GSM914502", "GSM914503", "GSM914504", "GSM914505", "GSM914506", "GSM914507", "GSM914508", "GSM914509", "GSM914510", "GSM914511", "GSM914512", "GSM914513", "GSM914514", "GSM914515", "GSM914516", "GSM914517", "GSM914518", "GSM914519", "GSM914520", "GSM914521", "GSM914522", "GSM914523", "GSM914524", "GSM914525", "GSM914526", "GSM914527", "GSM914528", "GSM914529", "GSM914530", "GSM914531", "GSM914532", "GSM914533", "GSM914534", "GSM914535", "GSM914536", "GSM914537", "GSM914538", "GSM914539", "GSM914540", "GSM914541", "GSM914542", "GSM914543", "GSM914544", "GSM914545", "GSM914546", "GSM914547", "GSM914548", "GSM914549", "GSM914550", "GSM914551", "GSM914552", "GSM914553", "GSM914554", "GSM914555", "GSM914556", "GSM914557", "GSM914558", "GSM914559", "GSM914560", "GSM914561", "GSM914562", "GSM914563", "GSM914564", "GSM914565", "GSM914566", "GSM914567", "GSM914568", "GSM914569", "GSM914570", "GSM914571", "GSM914572", "GSM914573", "GSM914574", "GSM914575", "GSM914576", "GSM914577", "GSM914578", "GSM914579", "GSM914580", "GSM914581", "GSM914582", "GSM914583", "GSM914584", "GSM914585", "GSM914586", "GSM914587", "GSM914588", "GSM914589", "GSM914590", "GSM914591", "GSM914592", "GSM914593", "GSM914594", "GSM914595", "GSM914596", "GSM914597", "GSM914598", "GSM914599", "GSM914600", "GSM914601", "GSM914602", "GSM914603", "GSM914604", "GSM914605", "GSM914606", "GSM914607", "GSM914608", "GSM914609", "GSM914610", "GSM914611", "GSM914612", "GSM914613", "GSM914614", "GSM914615", "GSM914616", "GSM914617", "GSM914618", "GSM914619", "GSM914620", "GSM914621", "GSM914622", "GSM914623", "GSM914624", "GSM914625", "GSM914626", "GSM914627", "GSM914628", "GSM914629", "GSM914630", "GSM914631", "GSM914632", "GSM914633", "GSM914634", "GSM914635", "GSM914636", "GSM914637", "GSM914638", "GSM914639", "GSM914640", "GSM914641", "GSM914642", "GSM914643", "GSM914644", "GSM914645", "GSM914646", "GSM914647", "GSM914648", "GSM914649", "GSM914650", "GSM914651", "GSM914652", "GSM914653", "GSM914654", "GSM914655", "GSM914656", "GSM914657", "GSM914658", "GSM914659", "GSM914660", "GSM914661", "GSM914662", "GSM914663", "GSM914664", "GSM914665", "GSM914666", "GSM914667", "GSM914668", "GSM914669", "GSM914670", "GSM914671", "GSM914672", "GSM914673", "GSM914674", "GSM914675", "GSM914676", "GSM914677", "GSM914678", "GSM914679", "GSM914680", "GSM914681", "GSM914682", "GSM914683", "GSM914684", "GSM914685", "GSM914686", "GSM914687", "GSM914688", "GSM914689", "GSM914690", "GSM914691", "GSM914692", "GSM914693", "GSM914694", "GSM914695", "GSM914696", "GSM914697", "GSM914698", "GSM914699", "GSM914700", "GSM914701", "GSM914702", "GSM914703", "GSM914704", "GSM914705", "GSM914706", "GSM914707", "GSM914708", "GSM914709", "GSM914710", "GSM914711", "GSM914712", "GSM914713", "GSM914714", "GSM914715", "GSM914716", "GSM914717", "GSM914718", "GSM914719", "GSM914720", "GSM914721", "GSM914722", "GSM914723", "GSM914724", "GSM914725", "GSM914726", "GSM914727", "GSM914728", "GSM914729", "GSM914730", "GSM914731", "GSM914732", "GSM914733", "GSM914734", "GSM914735", "GSM914736", "GSM914737", "GSM914738", "GSM914739", "GSM914740", "GSM914741", "GSM914742", "GSM914743", "GSM914744", "GSM914745", "GSM914746", "GSM914747", "GSM914748", "GSM914749", "GSM914750", "GSM914751", "GSM914752", "GSM914753", "GSM914754", "GSM914755", "GSM914756", "GSM914757", "GSM914758", "GSM914759", "GSM914760", "GSM914761", "GSM914762", "GSM914763", "GSM914764", "GSM914765", "GSM914766", "GSM914767", "GSM914768", "GSM914769", "GSM914770", "GSM914771", "GSM914772", "GSM914773", "GSM914774", "GSM914775", "GSM914776", "GSM914777", "GSM914778", "GSM914779", "GSM914780", "GSM914781", "GSM914782", "GSM914783", "GSM914784", "GSM914785", "GSM914786", "GSM914787", "GSM914788", "GSM914789", "GSM914790", "GSM914791", "GSM914792", "GSM914793", "GSM914794", "GSM914795", "GSM914796", "GSM914797", "GSM914798", "GSM914799", "GSM914800", "GSM914801", "GSM914802", "GSM914803", "GSM914804", "GSM914805", "GSM914806", "GSM914807", "GSM914808", "GSM914809", "GSM914810", "GSM914811", "GSM914812", "GSM914813", "GSM914814", "GSM914815", "GSM914816", "GSM914817", "GSM914818", "GSM914819", "GSM914820", "GSM914821", "GSM914822", "GSM914823", "GSM914824", "GSM914825", "GSM914826", "GSM914827", "GSM914828", "GSM914829", "GSM914830", "GSM914831", "GSM914832", "GSM914833", "GSM914834", "GSM914835", "GSM914836", "GSM914837", "GSM914838", "GSM914839", "GSM914840", "GSM914841", "GSM914842", "GSM914843", "GSM914844", "GSM914845", "GSM914846", "GSM914847", "GSM914848", "GSM914849", "GSM914850", "GSM914851", "GSM914852", "GSM914853", "GSM914854", "GSM914855", "GSM914856", "GSM914857", "GSM914858", "GSM914859", "GSM914860", "GSM914861", "GSM914862", "GSM914863", "GSM914864", "GSM914865", "GSM914866", "GSM914867", "GSM914868", "GSM914869", "GSM914870", "GSM914871", "GSM914872", "GSM914873", "GSM914874", "GSM914875", "GSM914876", "GSM914877", "GSM914878", "GSM914879", "GSM914880", "GSM914881", "GSM914882", "GSM914883", "GSM914884", "GSM914885", "GSM914886", "GSM914887", "GSM914888", "GSM914889"], "sample_count": 537, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Genome-wide transcriptional profiling of HIV positive and negative adults with active tuberculosis, latent TB infection and other diseases", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39939", "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=GSE39939", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39939", "version": null, "note": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1249177", "GSM1249178", "GSM1249179", "GSM1249180", "GSM1249181", "GSM1249182", "GSM1249183", "GSM1249184", "GSM1249185", "GSM1249186", "GSM1249187", "GSM1249188", "GSM1249189", "GSM1249190", "GSM1249191", "GSM1249192", "GSM1249193", "GSM1249194", "GSM1249195", "GSM1249196", "GSM1249197", "GSM1249198", "GSM1249199", "GSM1249200", "GSM1249201", "GSM1249202", "GSM1249203", "GSM1249204", "GSM1249205", "GSM1249206", "GSM1249207", "GSM1249208", "GSM1249209", "GSM1249210", "GSM1249211", "GSM1249212", "GSM1249213", "GSM1249214", "GSM1249215", "GSM1249216", "GSM1249217", "GSM1249218", "GSM1249219", "GSM1249220", "GSM1249221", "GSM1249222", "GSM1249223", "GSM1249224", "GSM1249225", "GSM1249226", "GSM1249227", "GSM1249228", "GSM1249229", "GSM1249230", "GSM1249231", "GSM1249232", "GSM1249233", "GSM1249234", "GSM1249235", "GSM1249236", "GSM1249237", "GSM1249238", "GSM1249239", "GSM1249240", "GSM1249241", "GSM1249242", "GSM1249243", "GSM1249244", "GSM1249245", "GSM1249246", "GSM1249247", "GSM1249248", "GSM1249249", "GSM1249250", "GSM1249251", "GSM1249252", "GSM1249253", "GSM1249254", "GSM1249255", "GSM1249256", "GSM1249257", "GSM1249258", "GSM1249259", "GSM1249260", "GSM1249261", "GSM1249262", "GSM1249263", "GSM1249264", "GSM1249265", "GSM1249266", "GSM1249267", "GSM1249268", "GSM1249269", "GSM1249270", "GSM1249271", "GSM1249272", "GSM1249273", "GSM1249274", "GSM1249275", "GSM1249276", "GSM1249277", "GSM1249278", "GSM1249279", "GSM1249280", "GSM1249281", "GSM1249282", "GSM1249283", "GSM1249284", "GSM1249285", "GSM1249286", "GSM1249287", "GSM1249288", "GSM1249289", "GSM1249290", "GSM1249291", "GSM1249292", "GSM1249293", "GSM1249294", "GSM1249295", "GSM1249296", "GSM1249297", "GSM1249298", "GSM1249299", "GSM1249300", "GSM1249301", "GSM1249302", "GSM1249303", "GSM1249304", "GSM1249305", "GSM1249306", "GSM1249307", "GSM1249308", "GSM1249309", "GSM1249310", "GSM1249311", "GSM1249312", "GSM1249313", "GSM1249314", "GSM1249315", "GSM1249316", "GSM1249317", "GSM1249318", "GSM1249319", "GSM1249320", "GSM1249321", "GSM1249322", "GSM1249323", "GSM1249324", "GSM1249325", "GSM1249326", "GSM1249327", "GSM1249328", "GSM1249329", "GSM1249330", "GSM1249331", "GSM1249332", "GSM1249333"], "sample_count": 157, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Genome wide transcriptional profiling of HIV positive and negative children with active tuberculosis, latent TB infection and other diseases from Kenya", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39940", "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=GSE39940", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39940", "version": null, "note": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM981627", "GSM981628", "GSM981629", "GSM981630", "GSM981631", "GSM981632", "GSM981633", "GSM981634", "GSM981635", "GSM981636", "GSM981637", "GSM981638", "GSM981639", "GSM981640", "GSM981641", "GSM981642", "GSM981643", "GSM981644", "GSM981645", "GSM981646", "GSM981647", "GSM981648", "GSM981649", "GSM981650", "GSM981651", "GSM981652", "GSM981653", "GSM981654", "GSM981655", "GSM981656", "GSM981657", "GSM981658", "GSM981659", "GSM981660", "GSM981661", "GSM981662", "GSM981663", "GSM981664", "GSM981665", "GSM981666", "GSM981667", "GSM981668", "GSM981669", "GSM981670", "GSM981671", "GSM981672", "GSM981673", "GSM981674", "GSM981675", "GSM981676", "GSM981677", "GSM981678", "GSM981679", "GSM981680", "GSM981681", "GSM981682", "GSM981683", "GSM981684", "GSM981685", "GSM981686", "GSM981687", "GSM981688", "GSM981689", "GSM981690", "GSM981691", "GSM981692", "GSM981693", "GSM981694", "GSM981695", "GSM981696", "GSM981697", "GSM981698", "GSM981699", "GSM981700", "GSM981701", "GSM981702", "GSM981703", "GSM981704", "GSM981705", "GSM981706", "GSM981707", "GSM981708", "GSM981709", "GSM981710", "GSM981711", "GSM981712", "GSM981713", "GSM981714", "GSM981715", "GSM981716", "GSM981717", "GSM981718", "GSM981719", "GSM981720", "GSM981721", "GSM981722", "GSM981723", "GSM981724", "GSM981725", "GSM981726", "GSM981727", "GSM981728", "GSM981729", "GSM981730", "GSM981731", "GSM981732", "GSM981733", "GSM981734", "GSM981735", "GSM981736", "GSM981737", "GSM981738", "GSM981739", "GSM981740", "GSM981741", "GSM981742", "GSM981743", "GSM981744", "GSM981745", "GSM981746", "GSM981747", "GSM981748", "GSM981749", "GSM981750", "GSM981751", "GSM981752", "GSM981753", "GSM981754", "GSM981755", "GSM981756", "GSM981757", "GSM981758", "GSM981759", "GSM981760", "GSM981761", "GSM981762", "GSM981763", "GSM981764", "GSM981765", "GSM981766", "GSM981767", "GSM981768", "GSM981769", "GSM981770", "GSM981771", "GSM981772", "GSM981773", "GSM981774", "GSM981775", "GSM981776", "GSM981777", "GSM981778", "GSM981779", "GSM981780", "GSM981781", "GSM981782", "GSM981783", "GSM981784", "GSM981785", "GSM981786", "GSM981787", "GSM981788", "GSM981789", "GSM981790", "GSM981791", "GSM981792", "GSM981793", "GSM981794", "GSM981795", "GSM981796", "GSM981797", "GSM981798", "GSM981799", "GSM981800", "GSM981801", "GSM981802", "GSM981803", "GSM981804", "GSM981805", "GSM981806", "GSM981807", "GSM981808", "GSM981809", "GSM981810", "GSM981811", "GSM981812", "GSM981813", "GSM981814", "GSM981815", "GSM981816", "GSM981817", "GSM981818", "GSM981819", "GSM981820", "GSM981821", "GSM981822", "GSM981823", "GSM981824", "GSM981825", "GSM981826", "GSM981827", "GSM981828", "GSM981829", "GSM981830", "GSM981831", "GSM981832", "GSM981833", "GSM981834", "GSM981835", "GSM981836", "GSM981837", "GSM981838", "GSM981839", "GSM981840", "GSM981841", "GSM981842", "GSM981843", "GSM981844", "GSM981845", "GSM981846", "GSM981847", "GSM981848", "GSM981849", "GSM981850", "GSM981851", "GSM981852", "GSM981853", "GSM981854", "GSM981855", "GSM981856", "GSM981857", "GSM981858", "GSM981859", "GSM981860", "GSM981861", "GSM981862", "GSM981863", "GSM981864", "GSM981865", "GSM981866", "GSM981867", "GSM981868", "GSM981869", "GSM981870", "GSM981871", "GSM981872", "GSM981873", "GSM981874", "GSM981875", "GSM981876", "GSM981877", "GSM981878", "GSM981879", "GSM981880", "GSM981881", "GSM981882", "GSM981883", "GSM981884", "GSM981885", "GSM981886", "GSM981887", "GSM981888", "GSM981889", "GSM981890", "GSM981891", "GSM981892", "GSM981893", "GSM981894", "GSM981895", "GSM981896", "GSM981897", "GSM981898", "GSM981899", "GSM981900", "GSM981901", "GSM981902", "GSM981903", "GSM981904", "GSM981905", "GSM981906", "GSM981907", "GSM981908", "GSM981909", "GSM981910", "GSM981911", "GSM981912", "GSM981913", "GSM981914", "GSM981915", "GSM981916", "GSM981917", "GSM981918", "GSM981919", "GSM981920", "GSM981921", "GSM981922", "GSM981926", "GSM981927", "GSM981928", "GSM981929", "GSM981930", "GSM981931", "GSM981932", "GSM981933", "GSM981934", "GSM981935", "GSM981936", "GSM981937", "GSM981938", "GSM981939", "GSM981940", "GSM981941", "GSM981942", "GSM981943", "GSM981944", "GSM981945", "GSM981946", "GSM981947", "GSM981948", "GSM981949", "GSM981950", "GSM981951", "GSM981952", "GSM981953", "GSM981954", "GSM981955", "GSM981956", "GSM981957", "GSM981958", "GSM981959", "GSM981960", "GSM982065", "GSM982066", "GSM982067"], "sample_count": 334, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Genome wide transcriptional profiling of HIV positive and negative children with active tuberculosis, latent TB infection and other diseases from South Africa and Malawi", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE54992", "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=GSE54992", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54992", "version": null, "note": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1327526", "GSM1327527", "GSM1327528", "GSM1327529", "GSM1327530", "GSM1327531", "GSM1327532", "GSM1327533", "GSM1327534", "GSM1327535", "GSM1327536", "GSM1327537", "GSM1327538", "GSM1327539", "GSM1327540", "GSM1327541", "GSM1327542", "GSM1327543", "GSM1327544", "GSM1327545", "GSM1327546", "GSM1327547", "GSM1327548", "GSM1327549", "GSM1327550", "GSM1327551", "GSM1327552", "GSM1327553", "GSM1327554", "GSM1327555", "GSM1327556", "GSM1327557", "GSM1327558", "GSM1327559", "GSM1327560", "GSM1327561", "GSM1327562", "GSM1327563", "GSM1327564"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from peripheral blood", "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:GSE19444 not downloaded", "asset:data:geo:GSE19444 licence not read", "asset:data:geo:GSE37250 not downloaded", "asset:data:geo:GSE37250 licence not read", "asset:data:geo:GSE39939 not downloaded", "asset:data:geo:GSE39939 licence not read", "asset:data:geo:GSE39940 not downloaded", "asset:data:geo:GSE39940 licence not read", "asset:data:geo:GSE54992 not downloaded", "asset:data:geo:GSE54992 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The ‘limma’ package in the R software was used to identify the DEGs among latent and active TB samples. If |fold change|≥1 and P < 0.05, genes were considered to be differentially expressed. Finally, Pearson’s correlation analysis was used to identify genes related to monocyte abundance."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "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": ["method.reader_differs_from_extractor"]}, "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: limma_voom."}, "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": ["GSE54992", "GSE19444", "GSE37250", "GSE39939", "GSE39940"], "resolved_accessions": ["GSE54992", "GSE19444", "GSE37250", "GSE39939", "GSE39940"], "statements": ["The datasets analyzed during the present study are available from GEO database (http://www.ncbi.nlm.nih.gov/geo/). For further inquiries, please contact the corresponding author."], "basis": "The paper names GSE54992, GSE19444, GSE37250, GSE39939, GSE39940 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:34751089", "data:geo:GSE19444"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19444"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:06:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9822, "completion_tokens": 2440, "cached_tokens": 128}}, "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:34751089", "type": "paper", "label": "pmid:34751089"}, {"id": "source:pmid:34751089", "type": "manuscript", "label": "PMID 34751089 full text"}, {"id": "data:geo:GSE19444", "type": "dataset", "label": "GEO GSE19444"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34751089", "type": "paper", "label": "pmid:34751089"}, {"id": "source:pmid:34751089", "type": "manuscript", "label": "PMID 34751089 full text"}, {"id": "data:geo:GSE19444", "type": "dataset", "label": "GEO GSE19444"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34751089", "type": "extraction", "used": ["source:pmid:34751089"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19444", "type": "accession_resolution", "used": ["data:geo:GSE19444"], "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:34751089", "parent_hash": "sha256:5e749a689f3b0b03479a8be5325a0bce0a147249e2f196f66c2a41b9d77ad342", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE19444 licence not read", "asset:data:geo:GSE19444 not downloaded", "asset:data:geo:GSE37250 licence not read", "asset:data:geo:GSE37250 not downloaded", "asset:data:geo:GSE39939 licence not read", "asset:data:geo:GSE39939 not downloaded", "asset:data:geo:GSE39940 licence not read", "asset:data:geo:GSE39940 not downloaded", "asset:data:geo:GSE54992 licence not read", "asset:data:geo:GSE54992 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [") software. Verification in clinical samples RT-qPCR results showed that peripheral blood mononuc", "oftware. Verification in clinical samples RT-qPCR results showed that peripheral blood mononuc"], "order_basis": "paper_text_order:2269", "id": "assay:1"}, {"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": ["The ‘limma’ package in the R software was used to identify the DEGs among latent and active TB samples. If |fold change|≥1 and P < 0.05, genes were considered to be differentially expressed. Finally, Pearson’s correlation analysis was used to identify genes related to monocyte abundance."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}