The Identification of Childhood Asthma Progression-Related lncRNAs and mRNAs Suitable as Biomarkers Using Weighted Gene Coexpression Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34456632", "kind": "science-record", "revision": 7, "content_hash": "sha256:181c5a7166e9baa13c6d003c193e38bd2f0be5906ca0a2513f5a82e14b28dda2", "created_at": "2026-11-01T15:41:50Z", "updated_at": "2026-11-01T22:04:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Identification of Childhood Asthma Progression-Related lncRNAs and mRNAs Suitable as Biomarkers Using Weighted Gene Coexpression Network Analysis.", "doi": "10.1155/2021/5511507", "pmid": "34456632", "authors": ["Min Hao", "Jinling Zan"], "journal": "Genetics research", "year": 2021, "abstract": "Background: Asthma is a common chronic respiratory disease in children, seriously affecting children's health and growth. This bioinformatics study aimed to identify potential RNA candidates closely associated with childhood asthma development within current gene databases.\nMethods: GSE65204 and GSE19187 datasets were screened and downloaded from the NCBI GEO database. Differentially expressed long noncoding RNAs (DE-lncRNAs) and mRNAs (DE-mRNAs) were identified using the Bioconductor limma package in R, and these DE-mRNAs were used to perform biological process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Thereafter, weighted gene coexpression network analysis (WGCNA) was utilized to screen the modules directly related to childhood asthma, and a coexpression network of DE-lncRNAs and DE-mRNAs was built. Finally, principal component analysis (PCA) was performed.\nResults: In total, 7 DE-lncRNAs and 1060 DE-mRNAs, as well as 7 DE-lncRNAs and 1027 DE-mRNAs, were identified in GSE65204 and GSE19187, respectively. After comparison, 336 overlapping genes had the same trend of expression, including 2 overlapped DE-lncRNAs and 334 overlapped DE-mRNAs. These overlapped DE-mRNAs were enriched in 28 BP and 12 KEGG pathways. Eleven modules were obtained in GSE65204, and it was found that the purple, black, and yellow modules were significantly positively correlated with asthma development. Subsequently, a coexpression network including 63 DE-mRNAs and 2 DE-lncRNAs was built, and five KEGG pathways, containing 8 genes, were found to be directly associated with childhood asthma. The PCA further verified these results.\nConclusion: LncRNAs LINC01559 and SNHG8 and mRNAs VWF, LAMB3, LAMA4, CAV1, ALDH1A3, SMOX, GNG4, and PPARG were identified as biomarkers associated with the progression of childhood asthma.", "claims": [{"id": "claim-method", "statement": "PCA is a dimension reduction technique that transforms multiple variables into a few principal components that can reflect most of the information of the original variables [27].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34456632", "locator": "sections[7] \"2.5. Identification of RNAs Directly Related to Asthma and Principal Component Analysis (PCA)\" paragraph 3", "quote": "PCA is a dimension reduction technique that transforms multiple variables into a few principal components that can reflect most of the information of the original variables [27]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34456632", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request."}], "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:34456632"], "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:GSE19187"], "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:GSE19187"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34456632", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/5511507", "sha256": "sha256:b58a2a896b69e09919224d4adc11c86fc1b7971f7d7dae93bc2870b8914d5f78", "bytes": 24844, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/5511507", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8371738", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19187", "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=GSE19187", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19187", "version": null, "note": "The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM475618", "GSM475619", "GSM475620", "GSM475621", "GSM475622", "GSM475623", "GSM475624", "GSM475625", "GSM475626", "GSM475627", "GSM475628", "GSM475629", "GSM475630", "GSM475631", "GSM475632", "GSM475633", "GSM475634", "GSM475635", "GSM475636", "GSM475637", "GSM475638", "GSM475639", "GSM475640", "GSM475641", "GSM475642", "GSM475643", "GSM475644", "GSM475645", "GSM475646", "GSM475647", "GSM475648", "GSM475649", "GSM475650", "GSM475651", "GSM475652", "GSM475653", "GSM475654", "GSM475655"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Nasal epithelium gene expression profiling in child respiratory allergic disease", "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:GSE65204", "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=GSE65204", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65204", "version": null, "note": "The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1589502", "GSM1589503", "GSM1589504", "GSM1589505", "GSM1589506", "GSM1589507", "GSM1589508", "GSM1589509", "GSM1589510", "GSM1589511", "GSM1589512", "GSM1589513", "GSM1589514", "GSM1589515", "GSM1589516", "GSM1589517", "GSM1589518", "GSM1589519", "GSM1589520", "GSM1589521", "GSM1589522", "GSM1589523", "GSM1589524", "GSM1589525", "GSM1589526", "GSM1589527", "GSM1589528", "GSM1589529", "GSM1589530", "GSM1589531", "GSM1589532", "GSM1589533", "GSM1589534", "GSM1589535", "GSM1589536", "GSM1589537", "GSM1589538", "GSM1589539", "GSM1589540", "GSM1589541", "GSM1589542", "GSM1589543", "GSM1589544", "GSM1589545", "GSM1589546", "GSM1589547", "GSM1589548", "GSM1589549", "GSM1589550", "GSM1589551", "GSM1589552", "GSM1589553", "GSM1589554", "GSM1589555", "GSM1589556", "GSM1589557", "GSM1589558", "GSM1589559", "GSM1589560", "GSM1589561", "GSM1589562", "GSM1589563", "GSM1589564", "GSM1589565", "GSM1589566", "GSM1589567", "GSM1589568", "GSM1589569", "GSM1589570"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "14550", "taxon": "Homo sapiens", "title": "The Nasal Gene Expression and Childhood Atopic Asthma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE19187 not downloaded", "asset:data:geo:GSE19187 licence not read", "asset:data:geo:GSE65204 not downloaded", "asset:data:geo:GSE65204 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "PCA is a dimension reduction technique that transforms multiple variables into a few principal components that can reflect most of the information of the original variables [27]."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "limma"}}], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE65204", "GSE19187"], "resolved_accessions": ["GSE65204", "GSE19187"], "statements": ["The datasets used and/or analyzed in this study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE65204, GSE19187 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:34456632", "data:geo:GSE19187"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19187"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 19553, "completion_tokens": 1523, "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:34456632", "type": "paper", "label": "pmid:34456632"}, {"id": "source:pmid:34456632", "type": "manuscript", "label": "PMID 34456632 full text"}, {"id": "data:geo:GSE19187", "type": "dataset", "label": "GEO GSE19187"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34456632", "type": "paper", "label": "pmid:34456632"}, {"id": "source:pmid:34456632", "type": "manuscript", "label": "PMID 34456632 full text"}, {"id": "data:geo:GSE19187", "type": "dataset", "label": "GEO GSE19187"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34456632", "type": "extraction", "used": ["source:pmid:34456632"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19187", "type": "accession_resolution", "used": ["data:geo:GSE19187"], "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:34456632", "parent_hash": "sha256:7096ed8dee61054a9be0afdb9292054e0d98c64b94fb87dbd04fea6c130706bc", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE19187 licence not read", "asset:data:geo:GSE19187 not downloaded", "asset:data:geo:GSE65204 licence not read", "asset:data:geo:GSE65204 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["PCA is a dimension reduction technique that transforms multiple variables into a few principal components that can reflect most of the information of the original variables [27]."], "order_basis": "analysis_only", "id": "assay:1"}]}