Single-cell combined with transcriptome sequencing to explore the molecular mechanism of cell communication in idiopathic pulmonary fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38887981", "kind": "science-record", "revision": 2, "content_hash": "sha256:c3738f357746ae0eebdfe7c61f190c0f1b036cdea1a83811c0dbf872202ab595", "created_at": "2026-11-01T20:28:57Z", "updated_at": "2026-11-01T21:33:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell combined with transcriptome sequencing to explore the molecular mechanism of cell communication in idiopathic pulmonary fibrosis.", "doi": "10.1111/jcmm.18499", "pmid": "38887981", "authors": ["Minggao Zhu", "Yuhu Yi", "Kui Jiang", "Yongzhi Liang", "Lijun Li", "Feng Zhang", "Xinglong Zheng", "Haiyan Yin"], "journal": "Journal of cellular and molecular medicine", "year": 2024, "abstract": "Idiopathic pulmonary fibrosis (IPF) is a common, chronic, and progressive lung disease that severely impacts human health and survival. However, the intricate molecular underpinnings of IPF remains elusive. This study aims to delve into the nuanced molecular interplay of cellular interactions in IPF, thereby laying the groundwork for innovative therapeutic approaches in the clinical field of IPF. Sophisticated bioinformatics methods were employed to identify crucial biomarkers essential for the progression of IPF. The GSE122960 single-cell dataset was obtained from the Gene Expression Omnibus (GEO) compendium, and intercellular communication potentialities were scrutinized via CellChat. The random survival forest paradigm was established using the GSE70866 dataset. Quintessential genes were selected through Kaplan-Meier (KM) curves, while immune infiltration examinations, functional enrichment critiques and nomogram paradigms were inaugurated. Analysis of intercellular communication revealed an intimate potential connections between macrophages and various cell types, pinpointing five cardinal genes influencing the trajectory and prognosis of IPF. The nomogram paradigm, sculpted from these seminal genes, exhibits superior predictive prowess. Our research meticulously identified five critical genes, confirming their intimate association with the prognosis, immune infiltration and transcriptional governance of IPF. Interestingly, we discerned these genes' engagement with the EPITHELIAL_MESENCHYMAL_TRANSITION signalling pathway, which may enhance our understanding of the molecular complexity of IPF.", "claims": [{"id": "claim-method", "statement": "We utilized the RSF algorithm, a machine learning approach, to sift through hallmark genes employing the randomForestSRC suite.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38887981", "locator": "sections[6] \"Random survival forest algorithm\" paragraph 2", "quote": "We utilized the RSF algorithm, a machine learning approach, to sift through hallmark genes employing the randomForestSRC suite."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38887981", "locator": "sections[32] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our research meticulously identified five critical genes, confirming their intimate association with the prognosis, immune infiltration and transcriptional governance of IPF.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38887981", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our research meticulously identified five critical genes, confirming their intimate association with the prognosis, immune infiltration and transcriptional governance of IPF."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our research meticulously identified five critical genes, confirming their intimate association with the prognosis, immune infiltration and transcriptional governance of IPF.", "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:38887981"], "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:GSE122960"], "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:GSE122960"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38887981", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.18499", "sha256": "sha256:97934fddbed75c86fdae15ceaef4155ff2c4def67c5c082c39dca44446002219", "bytes": 37041, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/jcmm.18499", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11184282", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE122960", "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=GSE122960", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE122960", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3489182", "GSM3489183", "GSM3489184", "GSM3489185", "GSM3489186", "GSM3489187", "GSM3489188", "GSM3489189", "GSM3489190", "GSM3489191", "GSM3489192", "GSM3489193", "GSM3489194", "GSM3489195", "GSM3489196", "GSM3489197", "GSM3489198"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis II", "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:GSE70866", "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=GSE70866", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70866", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1820719", "GSM1820720", "GSM1820721", "GSM1820722", "GSM1820723", "GSM1820724", "GSM1820725", "GSM1820726", "GSM1820727", "GSM1820728", "GSM1820729", "GSM1820730", "GSM1820731", "GSM1820732", "GSM1820733", "GSM1820734", "GSM1820735", "GSM1820736", "GSM1820737", "GSM1820738", "GSM1820739", "GSM1820740", "GSM1820741", "GSM1820742", "GSM1820743", "GSM1820744", "GSM1820745", "GSM1820746", "GSM1820747", "GSM1820748", "GSM1820749", "GSM1820750", "GSM1820751", "GSM1820752", "GSM1820753", "GSM1820754", "GSM1820755", "GSM1820756", "GSM1820757", "GSM1820758", "GSM1820759", "GSM1820760", "GSM1820761", "GSM1820762", "GSM1820763", "GSM1820764", "GSM1820765", "GSM1820766", "GSM1820767", "GSM1820768", "GSM1820769", "GSM1820770", "GSM1820771", "GSM1820772", "GSM1820773", "GSM1820774", "GSM1820775", "GSM1820776", "GSM1820777", "GSM1820778", "GSM1820779", "GSM1820780", "GSM1820781", "GSM1820782", "GSM1820783", "GSM1820784", "GSM1820785", "GSM1820786", "GSM1820787", "GSM1820788", "GSM1820789", "GSM1820790", "GSM1820791", "GSM1820792", "GSM1820793", "GSM1820794", "GSM1820795", "GSM1820796", "GSM1820797", "GSM1820798", "GSM1820799", "GSM1820800", "GSM1820801", "GSM1820802", "GSM1820803", "GSM1820804", "GSM1820805", "GSM1820806", "GSM1820807", "GSM1820808", "GSM1820809", "GSM1820810", "GSM1820811", "GSM1820812", "GSM1820813", "GSM1820814", "GSM1820815", "GSM1820816", "GSM1820817", "GSM1820818", "GSM1820819", "GSM1820820", "GSM1820821", "GSM1820822", "GSM1820823", "GSM1820824", "GSM1820825", "GSM1820826", "GSM1820827", "GSM1820828", "GSM1820829", "GSM1820830", "GSM1820831", "GSM1820832", "GSM1820833", "GSM1820834", "GSM1820835", "GSM1820836", "GSM1820837", "GSM1820838", "GSM1820839", "GSM1820840", "GSM1820841", "GSM1820842", "GSM1820843", "GSM1820844", "GSM1820845", "GSM1820846", "GSM1820847", "GSM1820848", "GSM1820849", "GSM1820850", "GSM1820851", "GSM1820852", "GSM1820853", "GSM1820854", "GSM1820855", "GSM1820856", "GSM1820857", "GSM1820858", "GSM1820859", "GSM1820860", "GSM1820861", "GSM1820862", "GSM1820863", "GSM1820864", "GSM1820865", "GSM1820866", "GSM1820867", "GSM1820868", "GSM1820869", "GSM1820870", "GSM1820871", "GSM1820872", "GSM1820873", "GSM1820874", "GSM1820875", "GSM1820876", "GSM1820877", "GSM1820878", "GSM1820879", "GSM1820880", "GSM1820881", "GSM1820882", "GSM1820883", "GSM1820884", "GSM1820885", "GSM1820886", "GSM1820887", "GSM1820888", "GSM1820889", "GSM1820890", "GSM1820891", "GSM1820892", "GSM1820893", "GSM1820894", "GSM1820895", "GSM1820896", "GSM1820897", "GSM1820898", "GSM1820899", "GSM1820900", "GSM1820901", "GSM1820902", "GSM1820903", "GSM1820904", "GSM1820905", "GSM1820906", "GSM1820907", "GSM1820908", "GSM1820909", "GSM1820910", "GSM1820911", "GSM1820912", "GSM1820913", "GSM1820914"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "17077;14550", "taxon": "Homo sapiens", "title": "BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (II)", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE122960 not downloaded", "asset:data:geo:GSE122960 licence not read", "asset:data:geo:GSE70866 not downloaded", "asset:data:geo:GSE70866 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": null, "specific": null, "label": "random survival forest (RSF) algorithm", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We utilized the RSF algorithm, a machine learning approach, to sift through hallmark genes employing the randomForestSRC suite."}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE122960", "GSE70866"], "resolved_accessions": ["GSE122960", "GSE70866"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repositories/repositories and accession number(s) can be found in the article/supplementary material."], "basis": "The paper names GSE122960, GSE70866 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:38887981", "data:geo:GSE122960"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE122960"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:21:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9895, "completion_tokens": 1409, "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:38887981", "type": "paper", "label": "pmid:38887981"}, {"id": "source:pmid:38887981", "type": "manuscript", "label": "PMID 38887981 full text"}, {"id": "data:geo:GSE122960", "type": "dataset", "label": "GEO GSE122960"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38887981", "type": "paper", "label": "pmid:38887981"}, {"id": "source:pmid:38887981", "type": "manuscript", "label": "PMID 38887981 full text"}, {"id": "data:geo:GSE122960", "type": "dataset", "label": "GEO GSE122960"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38887981", "type": "extraction", "used": ["source:pmid:38887981"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE122960", "type": "accession_resolution", "used": ["data:geo:GSE122960"], "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:38887981", "parent_hash": "sha256:71cbdacf6f51a9dca727efbc12c8b0483840e2bc6521b05d6f0f5adf557c9aeb", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE122960 licence not read", "asset:data:geo:GSE122960 not downloaded", "asset:data:geo:GSE70866 licence not read", "asset:data:geo:GSE70866 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}