← All .science files
pmid:34213077
IRF1 as a potential biomarker in Mycobacterium tuberculosis infection.
Liwei Wu · Qiliang Cheng · Zilu Wen · Yanzheng Song · Yijun Zhu · Lin Wang
Journal of cellular and molecular medicine · 2021 doi:10.1111/jcmm.16756
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
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 · 6 items
claims array · 2 items
[0] object · 6 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 · 1 item
data object · 3 fields
assets array · 7 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 43 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 498 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 44 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 202 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
gaps array · 8 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
[1] 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 · 1 item
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 · 0 items
missing_operations array · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 4 items
resolved_accessions array · 4 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
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 · 14 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 · 0 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:34213077", "kind": "science-record", "revision": 7, "content_hash": "sha256:1b60d2604214c56866779741ceee4cf7bf64f5ef2495133b31fcba8ccb4fd4c2", "created_at": "2026-11-01T15:41:41Z", "updated_at": "2026-11-01T22:04:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "IRF1 as a potential biomarker in Mycobacterium tuberculosis infection.", "doi": "10.1111/jcmm.16756", "pmid": "34213077", "authors": ["Liwei Wu", "Qiliang Cheng", "Zilu Wen", "Yanzheng Song", "Yijun Zhu", "Lin Wang"], "journal": "Journal of cellular and molecular medicine", "year": 2021, "abstract": "Pulmonary tuberculosis (PTB) is a major global public health problem. The purpose of this study was to find biomarkers that can be used to diagnose tuberculosis. We used four NCBI GEO data sets to conduct analysis. Among the four data sets, GSE139825 is lung tissue microarray, and GSE83456, GSE19491 and GSE50834 are blood microarray. The differential genes of GSE139825 and GSE83456 were 68 and 226, and intersection genes were 11. Gene ontology (GO) analyses of 11 intersection genes revealed that the changes were mostly enriched in regulation of leucocyte cell-cell adhesion and regulation of T-cell activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs revealed that the host response in TB strongly involves cytokine-cytokine receptor interactions and folate biosynthesis. In order to further narrow the range of biomarkers, we used protein-protein interaction to establish a hub gene network of two data sets and a network of 11 candidate genes. Eventually, IRF1 was selected as a biomarker. As validation, IRF1 levels were shown to be up-regulated in patients with TB relative to healthy controls in data sets GSE19491 and GSE50834. Additionally, IRF1 levels were measured in the new patient samples using ELISA. IRF1 was seen to be significantly up-regulated in patients with TB compared with healthy controls with an AUC of 0.801. These results collectively indicate that IRF1 could serve as a new biomarker for the diagnosis of pulmonary tuberculosis.", "claims": [{"id": "claim-method", "statement": "Student t test was used to test the difference between the two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34213077", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "Student t test was used to test the difference between the two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34213077", "locator": "sections[21] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34213077"], "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:GSE139825"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE139825"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34213077", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.16756", "sha256": "sha256:360fd1a746b9f1cbc0202a7d0b6a552e192d5b3a2c7312a794262fbbcfbb0cca", "bytes": 20933, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/jcmm.16756", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8335664", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE139825", "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=GSE139825", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE139825", "version": null, "note": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4146976", "GSM4146977", "GSM4146978", "GSM4146979", "GSM4146980", "GSM4146981", "GSM4146982", "GSM4146983", "GSM4146984", "GSM4146985", "GSM4146986", "GSM4146987", "GSM4146988", "GSM4146989", "GSM4146990", "GSM4146991", "GSM4146992", "GSM4146993", "GSM4146994", "GSM4146995", "GSM4146996", "GSM4146997", "GSM4146998", "GSM4146999", "GSM4147000", "GSM4147001", "GSM4147002", "GSM4147003", "GSM4147004", "GSM4147005", "GSM4147006", "GSM4147007", "GSM4147008", "GSM4147009", "GSM4147010", "GSM4147011", "GSM4147012", "GSM4147013", "GSM4147014", "GSM4147015", "GSM4147016", "GSM4147017", "GSM4147018"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Human alveolar and splenic macrophage populations display a disctinct transcriptomic response to infection with Mycobacterium tuberculosis", "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:GSE19491", "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=GSE19491", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19491", "version": null, "note": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM484368", "GSM484369", "GSM484370", "GSM484371", "GSM484372", "GSM484373", "GSM484374", "GSM484375", "GSM484376", "GSM484377", "GSM484378", "GSM484379", "GSM484380", "GSM484381", "GSM484382", "GSM484383", "GSM484384", "GSM484385", "GSM484386", "GSM484387", "GSM484388", "GSM484389", "GSM484390", "GSM484391", "GSM484392", "GSM484393", "GSM484394", "GSM484395", "GSM484396", "GSM484397", "GSM484398", "GSM484399", "GSM484400", "GSM484448", "GSM484449", "GSM484450", "GSM484451", "GSM484452", "GSM484453", "GSM484454", "GSM484455", "GSM484456", "GSM484457", "GSM484458", "GSM484459", "GSM484460", "GSM484461", "GSM484462", "GSM484463", "GSM484464", "GSM484465", "GSM484466", "GSM484467", "GSM484468", "GSM484469", "GSM484470", "GSM484471", "GSM484472", "GSM484473", "GSM484474", "GSM484475", "GSM484476", "GSM484477", "GSM484478", "GSM484479", "GSM484480", "GSM484481", "GSM484482", "GSM484483", "GSM484484", "GSM484485", "GSM484486", "GSM484487", "GSM484488", "GSM484489", "GSM484500", "GSM484501", "GSM484502", "GSM484503", "GSM484504", "GSM484505", "GSM484506", "GSM484507", "GSM484508", "GSM484509", "GSM484510", "GSM484511", "GSM484512", "GSM484513", "GSM484514", "GSM484515", "GSM484516", "GSM484517", "GSM484518", "GSM484519", "GSM484520", "GSM484521", "GSM484522", "GSM484523", "GSM484524", "GSM484525", "GSM484526", "GSM484527", "GSM484528", "GSM484529", "GSM484530", "GSM484531", "GSM484532", "GSM484533", "GSM484534", "GSM484535", "GSM484536", "GSM484537", "GSM484538", "GSM484539", "GSM484540", "GSM484541", "GSM484542", "GSM484543", "GSM484544", "GSM484545", "GSM484546", "GSM484547", "GSM484548", "GSM484549", "GSM484550", "GSM484551", "GSM484552", "GSM484553", "GSM484554", "GSM484555", "GSM484556", "GSM484557", "GSM484558", "GSM484559", "GSM484560", "GSM484561", "GSM484562", "GSM484563", "GSM484564", "GSM484565", "GSM484566", "GSM484567", "GSM484568", "GSM484569", "GSM484570", "GSM484571", "GSM484572", "GSM484573", "GSM484574", "GSM484575", "GSM484576", "GSM484577", "GSM484578", "GSM484579", "GSM484580", "GSM484581", "GSM484582", "GSM484583", "GSM484584", "GSM484585", "GSM484586", "GSM484587", "GSM484588", "GSM484589", "GSM484590", "GSM484591", "GSM484592", "GSM484593", "GSM484594", "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", "GSM549324", "GSM549325", "GSM549326", "GSM549327", "GSM549328", "GSM549329", "GSM549331", "GSM549333", "GSM549335", "GSM549336", "GSM549338", "GSM549340", "GSM549342", "GSM549344", "GSM549345", "GSM549346", "GSM549347", "GSM549348", "GSM549349", "GSM549350", "GSM549351", "GSM549352", "GSM549353", "GSM549354", "GSM549355", "GSM549356", "GSM549357", "GSM549358", "GSM549359", "GSM549360", "GSM549361", "GSM549362", "GSM549363", "GSM549364", "GSM549365", "GSM549366", "GSM549367", "GSM549368", "GSM549369", "GSM549370", "GSM549371", "GSM549372", "GSM549373", "GSM549374", "GSM549375", "GSM549376", "GSM549377", "GSM549378", "GSM549379", "GSM549380", "GSM549381", "GSM549382", "GSM549383", "GSM549384", "GSM549385", "GSM549386", "GSM549387", "GSM549388", "GSM549389", "GSM549390", "GSM549391", "GSM549392", "GSM549393", "GSM549394", "GSM549395", "GSM549396", "GSM549397", "GSM549398", "GSM549399", "GSM549400", "GSM549401", "GSM549402", "GSM549403", "GSM549404", "GSM549405", "GSM549406", "GSM549407", "GSM549408", "GSM549409", "GSM549410", "GSM549411", "GSM549412", "GSM549413", "GSM549414", "GSM549415", "GSM549416", "GSM549417", "GSM549418", "GSM549419", "GSM549420", "GSM549421", "GSM549422", "GSM549423", "GSM549424", "GSM549425", "GSM549426", "GSM549427", "GSM549428", "GSM549429", "GSM549430", "GSM549431", "GSM549432", "GSM549433", "GSM549434", "GSM549435", "GSM549436", "GSM549437", "GSM549438", "GSM549439", "GSM549440", "GSM549441", "GSM549442", "GSM549443", "GSM549444", "GSM549445", "GSM549446", "GSM549447", "GSM549448", "GSM549449", "GSM549450", "GSM549451", "GSM549452", "GSM549453", "GSM549454", "GSM549455", "GSM549456", "GSM549457", "GSM549458", "GSM549459", "GSM549460", "GSM549461", "GSM549462", "GSM549463", "GSM549464", "GSM549465", "GSM549466", "GSM549467", "GSM549468", "GSM549469", "GSM549470", "GSM549471", "GSM549472", "GSM549473", "GSM549474", "GSM549475", "GSM549476", "GSM549477", "GSM549478", "GSM549479", "GSM549480", "GSM549481", "GSM549482", "GSM549483", "GSM549484", "GSM549485", "GSM549486", "GSM549487", "GSM549488", "GSM549489", "GSM549490", "GSM549491", "GSM549492", "GSM549493", "GSM549494", "GSM549495", "GSM549496", "GSM549497", "GSM549498", "GSM549499", "GSM549500", "GSM549501", "GSM549502", "GSM549503", "GSM549504", "GSM549505", "GSM549506", "GSM549507", "GSM549508", "GSM549509", "GSM549510", "GSM549511", "GSM549512", "GSM549513", "GSM549514", "GSM549515", "GSM549516", "GSM549517", "GSM549518", "GSM549519", "GSM549520", "GSM549521", "GSM549522", "GSM549523", "GSM550320", "GSM550321", "GSM550322", "GSM550323", "GSM550324", "GSM550325", "GSM550326", "GSM550327", "GSM550328", "GSM550329", "GSM550330", "GSM550331", "GSM550332", "GSM550333", "GSM550334", "GSM550335", "GSM550336", "GSM550337", "GSM550338", "GSM550339", "GSM550340", "GSM550341", "GSM550342", "GSM550343", "GSM550344", "GSM550345", "GSM550346", "GSM550347", "GSM550348", "GSM550349", "GSM550350", "GSM550351", "GSM550352", "GSM550353", "GSM550354", "GSM550355", "GSM550356", "GSM550357", "GSM550358", "GSM550359", "GSM550360", "GSM550361", "GSM550362", "GSM550363", "GSM550364", "GSM550365", "GSM550366", "GSM550367", "GSM550368", "GSM550369", "GSM550370", "GSM550371", "GSM550372", "GSM550373", "GSM550374", "GSM550375", "GSM550376", "GSM550377", "GSM550378", "GSM550379", "GSM550380", "GSM550381", "GSM550382", "GSM550383", "GSM550384", "GSM550385", "GSM550386", "GSM550387", "GSM550388", "GSM550389", "GSM550390", "GSM550391", "GSM550392", "GSM550393", "GSM550394", "GSM550395", "GSM550396", "GSM550397", "GSM550398", "GSM550399", "GSM550400"], "sample_count": 498, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Blood Transcriptional Profiles in Human Active and Latent Tuberculosis", "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:GSE50834", "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=GSE50834", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50834", "version": null, "note": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1230902", "GSM1230903", "GSM1230904", "GSM1230905", "GSM1230906", "GSM1230907", "GSM1230908", "GSM1230909", "GSM1230910", "GSM1230911", "GSM1230912", "GSM1230913", "GSM1230914", "GSM1230915", "GSM1230916", "GSM1230917", "GSM1230918", "GSM1230919", "GSM1230920", "GSM1230921", "GSM1230922", "GSM1230923", "GSM1230924", "GSM1230925", "GSM1230926", "GSM1230927", "GSM1230928", "GSM1230929", "GSM1230930", "GSM1230931", "GSM1230932", "GSM1230933", "GSM1230934", "GSM1230935", "GSM1230936", "GSM1230937", "GSM1230938", "GSM1230939", "GSM1230940", "GSM1230941", "GSM1230942", "GSM1230943", "GSM1230944", "GSM1230945"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression analysis of PBMC from HIV and HIV/TB co-infected patients", "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:GSE83456", "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=GSE83456", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE83456", "version": null, "note": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2203540", "GSM2203541", "GSM2203542", "GSM2203543", "GSM2203544", "GSM2203545", "GSM2203546", "GSM2203547", "GSM2203548", "GSM2203549", "GSM2203550", "GSM2203551", "GSM2203552", "GSM2203553", "GSM2203554", "GSM2203555", "GSM2203556", "GSM2203557", "GSM2203558", "GSM2203559", "GSM2203560", "GSM2203561", "GSM2203562", "GSM2203563", "GSM2203564", "GSM2203565", "GSM2203566", "GSM2203567", "GSM2203568", "GSM2203569", "GSM2203570", "GSM2203571", "GSM2203572", "GSM2203573", "GSM2203574", "GSM2203575", "GSM2203576", "GSM2203577", "GSM2203578", "GSM2203579", "GSM2203580", "GSM2203581", "GSM2203582", "GSM2203583", "GSM2203584", "GSM2203585", "GSM2203586", "GSM2203587", "GSM2203588", "GSM2203589", "GSM2203590", "GSM2203591", "GSM2203592", "GSM2203593", "GSM2203594", "GSM2203595", "GSM2203596", "GSM2203597", "GSM2203598", "GSM2203599", "GSM2203600", "GSM2203601", "GSM2203602", "GSM2203603", "GSM2203604", "GSM2203605", "GSM2203606", "GSM2203607", "GSM2203608", "GSM2203609", "GSM2203610", "GSM2203611", "GSM2203612", "GSM2203613", "GSM2203614", "GSM2203615", "GSM2203616", "GSM2203617", "GSM2203618", "GSM2203619", "GSM2203620", "GSM2203621", "GSM2203622", "GSM2203623", "GSM2203624", "GSM2203625", "GSM2203626", "GSM2203627", "GSM2203628", "GSM2203629", "GSM2203630", "GSM2203631", "GSM2203632", "GSM2203633", "GSM2203634", "GSM2203635", "GSM2203636", "GSM2203637", "GSM2203638", "GSM2203639", "GSM2203640", "GSM2203641", "GSM2203642", "GSM2203643", "GSM2203644", "GSM2203645", "GSM2203646", "GSM2203647", "GSM2203648", "GSM2203649", "GSM2203650", "GSM2203651", "GSM2203652", "GSM2203653", "GSM2203654", "GSM2203655", "GSM2203656", "GSM2203657", "GSM2203658", "GSM2203659", "GSM2203660", "GSM2203661", "GSM2203662", "GSM2203663", "GSM2203664", "GSM2203665", "GSM2203666", "GSM2203667", "GSM2203668", "GSM2203669", "GSM2203670", "GSM2203671", "GSM2203672", "GSM2203673", "GSM2203674", "GSM2203675", "GSM2203676", "GSM2203677", "GSM2203678", "GSM2203679", "GSM2203680", "GSM2203681", "GSM2203682", "GSM2203683", "GSM2203684", "GSM2203685", "GSM2203686", "GSM2203687", "GSM2203688", "GSM2203689", "GSM2203690", "GSM2203691", "GSM2203692", "GSM2203693", "GSM2203694", "GSM2203695", "GSM2203696", "GSM2203697", "GSM2203698", "GSM2203699", "GSM2203700", "GSM2203701", "GSM2203702", "GSM2203703", "GSM2203704", "GSM2203705", "GSM2203706", "GSM2203707", "GSM2203708", "GSM2203709", "GSM2203710", "GSM2203711", "GSM2203712", "GSM2203713", "GSM2203714", "GSM2203715", "GSM2203716", "GSM2203717", "GSM2203718", "GSM2203719", "GSM2203720", "GSM2203721", "GSM2203722", "GSM2203723", "GSM2203724", "GSM2203725", "GSM2203726", "GSM2203727", "GSM2203728", "GSM2203729", "GSM2203730", "GSM2203731", "GSM2203732", "GSM2203733", "GSM2203734", "GSM2203735", "GSM2203736", "GSM2203737", "GSM2203738", "GSM2203739", "GSM2203740", "GSM2203741"], "sample_count": 202, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "The transcriptional signature of active tuberculosis reflects symptom status in extra-pulmonary and pulmonary tuberculosis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34213077:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8367de9f11d2140279ab706007f05dbef3161d11c4a9a11a01c3416b702359f2", "bytes": 2049, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#jcmm16756-tbl-0001", "version": null, "note": "The GO and KEGG analysis of DEGs in GSE139825", "structure": {"pmcid": "PMC8335664", "section_index": 13, "section_title": "Enrichment analyses of DEGs", "row_count": 21, "column_count": 5}, "table": {"label": "TABLE 1", "caption": "The GO and KEGG analysis of DEGs in GSE139825", "rows": [["Category", "Description", "Count", "Log10(P)", "Log10(q)"], ["GO Biological Processes", "response to lipopolysaccharide", "26", "−31.99", "−27.62"], ["GO Biological Processes", "cellular response to interleukin‐1", "18", "−23.71", "−20.13"], ["GO Biological Processes", "positive regulation of cytokine production", "20", "−19.21", "−16.02"], ["GO Biological Processes", "defence response to other organism", "21", "−18.08", "−15.04"], ["GO Biological Processes", "maintenance of location", "14", "−13.39", "−10.72"], ["GO Biological Processes", "interleukin‐1 beta production", "10", "−12.98", "−10.37"], ["GO Biological Processes", "positive regulation of MAPK cascade", "16", "−12.57", "−9.99"], ["GO Biological Processes", "positive regulation of leucocyte migration", "10", "−11.73", "−9.23"], ["GO Biological Processes", "regulation of multi‐organism process", "13", "−10.5", "−8.1"], ["GO Biological Processes", "lipopolysaccharide‐mediated signalling pathway", "7", "−9.95", "−7.61"], ["GO Biological Processes", "nitric oxide biosynthetic process", "7", "−9.04", "−6.79"], ["GO Biological Processes", "response to mechanical stimulus", "9", "−8.69", "−6.47"], ["GO Biological Processes", "regulation of interleukin‐2 production", "6", "−8.68", "−6.46"], ["GO Biological Processes", "response to inorganic substance", "12", "−7.95", "−5.83"], ["GO Biological Processes", "negative regulation of cytokine production", "9", "−6.56", "−4.62"], ["GO Cellular Components", "external side of plasma membrane", "10", "−7.19", "−5.15"], ["GO Molecular Functions", "CXCR chemokine receptor binding", "4", "−7.02", "−5.01"], ["KEGG Pathway", "NOD‐like receptor signalling pathway", "16", "−20.73", "−17.36"], ["KEGG Pathway", "Influenza A", "10", "−10.87", "−8.44"], ["KEGG Pathway", "Transcriptional mis regulation in cancer", "7", "−6.55", "−4.61"]], "row_count": 21, "column_count": 5, "numeric_cells": 65, "header_rows": 1, "locator": "section[13]/table-wrap[1]#jcmm16756-tbl-0001"}}, {"id": "asset:table:pmid:34213077:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0fb55a2ddcc539f36c082d00b4ca43aba5ba37a7015e8cfb1eed8152d1b6d2d4", "bytes": 2031, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#jcmm16756-tbl-0002", "version": null, "note": "The GO and KEGG analysis of DEGs in GSE83456", "structure": {"pmcid": "PMC8335664", "section_index": 13, "section_title": "Enrichment analyses of DEGs", "row_count": 21, "column_count": 5}, "table": {"label": "TABLE 2", "caption": "The GO and KEGG analysis of DEGs in GSE83456", "rows": [["Category", "Description", "Count", "Log10(P)", "Log10(q)"], ["GO Biological Processes", "defence response to other organism", "41", "−25.22", "−20.86"], ["GO Biological Processes", "regulation of innate immune response", "35", "−23.45", "−19.39"], ["GO Biological Processes", "response to bacterium", "34", "−15.67", "−12.31"], ["GO Biological Processes", "regulation of inflammatory response", "27", "−13.54", "−10.22"], ["GO Biological Processes", "response to interferon‐gamma", "18", "−13.36", "−10.07"], ["GO Biological Processes", "myeloid leucocyte activation", "29", "−13.03", "−9.78"], ["KEGG Pathway", "Systemic lupus erythematosus", "15", "−12.72", "−9.5"], ["GO Biological Processes", "regulation of immune effector process", "23", "−11.39", "−8.26"], ["GO Biological Processes", "regulation of cell activation", "25", "−10.05", "−7.23"], ["KEGG Pathway", "NOD‐like receptor signalling pathway", "14", "−10.04", "−7.23"], ["GO Biological Processes", "regulation of response to biotic stimulus", "13", "−9.75", "−7"], ["GO Biological Processes", "regulation of response to cytokine stimulus", "14", "−9.22", "−6.54"], ["GO Biological Processes", "positive regulation of interferon‐beta production", "7", "−8.52", "−5.9"], ["GO Biological Processes", "cytokine secretion", "11", "−8.06", "−5.52"], ["GO Biological Processes", "response to lipopolysaccharide", "16", "−7.94", "−5.41"], ["GO Biological Processes", "positive regulation of I‐kappa B kinase/NF‐kappa B signalling", "12", "−7.44", "−5"], ["KEGG Pathway", "Pertussis", "8", "−6.8", "−4.44"], ["GO Biological Processes", "response to interferon‐beta", "6", "−6.76", "−4.4"], ["GO Biological Processes", "regulation of interleukin‐12 production", "7", "−6.59", "−4.25"], ["GO Biological Processes", "response to tumour necrosis factor", "14", "−6.53", "−4.21"]], "row_count": 21, "column_count": 5, "numeric_cells": 63, "header_rows": 1, "locator": "section[13]/table-wrap[2]#jcmm16756-tbl-0002"}}], "gaps": ["asset:data:geo:GSE139825 not downloaded", "asset:data:geo:GSE139825 licence not read", "asset:data:geo:GSE19491 not downloaded", "asset:data:geo:GSE19491 licence not read", "asset:data:geo:GSE50834 not downloaded", "asset:data:geo:GSE50834 licence not read", "asset:data:geo:GSE83456 not downloaded", "asset:data:geo:GSE83456 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student t test was used to test the difference between the two groups."}}, {"id": "method-2", "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.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE139825", "GSE83456", "GSE19491", "GSE50834"], "resolved_accessions": ["GSE139825", "GSE83456", "GSE19491", "GSE50834"], "statements": ["The data that support the findings of this study are openly available in NCBI GEO database at https://www.ncbi.nlm.nih.gov/geo/"], "basis": "The paper names GSE139825, GSE83456, GSE19491, GSE50834 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:34213077", "data:geo:GSE139825", "asset:table:pmid:34213077:1", "asset:table:pmid:34213077:2"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE139825"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 15754, "completion_tokens": 1434, "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:34213077", "type": "paper", "label": "pmid:34213077"}, {"id": "source:pmid:34213077", "type": "manuscript", "label": "PMID 34213077 full text"}, {"id": "data:geo:GSE139825", "type": "dataset", "label": "GEO GSE139825"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34213077", "type": "paper", "label": "pmid:34213077"}, {"id": "source:pmid:34213077", "type": "manuscript", "label": "PMID 34213077 full text"}, {"id": "data:geo:GSE139825", "type": "dataset", "label": "GEO GSE139825"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34213077", "type": "extraction", "used": ["source:pmid:34213077"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE139825", "type": "accession_resolution", "used": ["data:geo:GSE139825"], "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:34213077", "parent_hash": "sha256:5fea1673ba97a5720571289d85fe8d3fb77c1a86df6a7dada9880ce7f64a31e5", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE139825 licence not read", "asset:data:geo:GSE139825 not downloaded", "asset:data:geo:GSE19491 licence not read", "asset:data:geo:GSE19491 not downloaded", "asset:data:geo:GSE50834 licence not read", "asset:data:geo:GSE50834 not downloaded", "asset:data:geo:GSE83456 licence not read", "asset:data:geo:GSE83456 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["re measured in the new patient samples using ELISA. IRF1 was seen to be significantly up-regula"], "order_basis": "paper_text_order:1274", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Student t test was used to test the difference between the two groups."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}