T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31223533", "kind": "science-record", "revision": 8, "content_hash": "sha256:5882c2cc9478aef2541b115a256d3508a6cec1d96e552a3fb0355b24be8a3bff", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T22:44:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection.", "doi": "10.7717/peerj.7089", "pmid": "31223533", "authors": ["Zuanhao Qian", "Zhenglei Zhang", "Yingying Wang"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Respiratory syncytial virus (RSV) is the main cause of respiratory tract infection, which seriously threatens the health and life of children. This study is conducted to reveal the rehabilitation mechanisms of RSV infection.\nMETHODS: E-MTAB-5195 dataset was downloaded from EBI ArrayExpress database, including 39 acute phase samples in the acute phase of infection and 21 samples in the recovery period. Using the limma package, differentially expressed RNAs (DE-RNAs) were analyzed. The significant modules were identified using WGCNA package, and the mRNAs in them were conducted with enrichment analysis using DAVID tool. Afterwards, co-expression network for the RNAs involved in the significant modules was built by Cytoscape software. Additionally, RSV-correlated pathways were searched from Comparative Toxicogenomics Database, and then the pathway network was constructed.\nRESULTS: There were 2,489 DE-RNAs between the two groups, including 2,386 DE-mRNAs and 103 DE-lncRNAs. The RNAs in the black, salmon, blue, tan and turquoise modules correlated with stage were taken as RNA set1. Meanwhile, the RNAs in brown, blue, magenta and pink modules related to disease severity were defined as RNA set2. In the pathway networks, CD40LG and RASGRP1 co-expressed with LINC00891/LINC00526/LINC01215 were involved in the T cell receptor signaling pathway, and IL1B, IL1R2, IL18, and IL18R1 co-expressed with BAIAP2-AS1/CRNDE/LINC01503/SMIM25 were implicated in cytokine-cytokine receptor interaction.\nCONCLUSION: LINC00891/LINC00526/LINC01215 co-expressed with CD40LG and RASGRP1 might affect the rehabilitation process of RSV infection through the T cell receptor signaling pathway. Besides, BAIAP2-AS1/CRNDE/LINC01503/SMIM25 co-expressed with IL1 and IL18 families might function in the clearance process after RSV infection via cytokine-cytokine receptor interaction.", "claims": [{"id": "claim-method", "statement": "Using the R package limma (version 3.34.0, https://bioconductor.org/packages/release/bioc/html/limma.html) (Ritchie et al., 2015), differential expression analysis for the two groups were carried out.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31223533", "locator": "sections[4] \"Differential expression analysis\" paragraph 3", "quote": "Using the R package limma (version 3.34.0, https://bioconductor.org/packages/release/bioc/html/limma.html) (Ritchie et al., 2015), differential expression analysis for the two groups were carried out."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:Raw data is available at EBI Array Express database under accession number E-MTAB-5195 here: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5195/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31223533", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:Raw data is available at EBI Array Express database under accession number E-MTAB-5195 here: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5195/."}], "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:31223533"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31223533", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.7089", "sha256": "sha256:93f87aed296cd6504b91b51bb90cba78a0740ca5200112a8b191f6067e9749a9", "bytes": 34630, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.7089", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6571000", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:31223533:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4620ec04a41a42a78edfa074e5748957688d55640e29606e7b4ccf3ab8b4ef30", "bytes": 1515, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#table-3", "version": null, "note": "The pathways enriched for the mRNAs in the co-expression networks for RNA set1 and RNA set2.", "structure": {"pmcid": "PMC6571000", "section_index": 6, "section_title": "Co-expression network analysis", "row_count": 22, "column_count": 4}, "table": {"label": "Table 3", "caption": "The pathways enriched for the mRNAs in the co-expression networks for RNA set1 and RNA set2.", "rows": [["Category", "Term", "Count", "P-value"], ["RNA set1", "hsa04640:Hematopoietic cell lineage", "15", "2.25E-06"], ["", "hsa05340:Primary immunodeficiency", "9", "2.89E-05"], ["", "hsa04660:T cell receptor signaling pathway", "15", "3.41E-05"], ["", "hsa04662:B cell receptor signaling pathway", "10", "1.60E-03"], ["", "hsa03010:Ribosome", "9", "1.41E-02"], ["", "hsa04514:Cell adhesion molecules (CAMs)", "9", "1.12E-02"], ["", "hsa04650:Natural killer cell mediated cytotoxicity", "9", "1.15E-02"], ["", "hsa05330:Allograft rejection", "4", "1.45E-02"], ["", "hsa00600:Sphingolipid metabolism", "4", "1.72E-02"], ["", "hsa04350:TGF-beta signaling pathway", "6", "2.15E-02"], ["RNA set2", "hsa00480:Glutathione metabolism", "7", "3.50E-03"], ["", "hsa04060:Cytokine-cytokine receptor interaction", "17", "4.80E-03"], ["", "hsa00600:Sphingolipid metabolism", "6", "5.70E-03"], ["", "hsa00052:Galactose metabolism", "5", "6.90E-03"], ["", "hsa04142:Lysosome", "10", "7.90E-03"], ["", "hsa04621:NOD-like receptor signaling pathway", "7", "1.00E-02"], ["", "hsa04640:Hematopoietic cell lineage", "8", "1.39E-02"], ["", "hsa00010:Glycolysis/Gluconeogenesis", "6", "3.26E-02"], ["", "hsa00500:Starch and sucrose metabolism", "5", "3.56E-02"], ["", "hsa00030:Pentose phosphate pathway", "4", "3.72E-02"], ["", "hsa00561:Glycerolipid metabolism", "5", "4.43E-01"]], "row_count": 22, "column_count": 4, "numeric_cells": 63, "header_rows": 1, "locator": "section[11]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:31223533:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b881d026905555cd5794ab0b5e0d526023269aa0759386c10d3a4c82100d385d", "bytes": 646, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#table-1", "version": null, "note": "The number and type of RNAs involved in each module.", "structure": {"pmcid": "PMC6571000", "section_index": 10, "section_title": "WGCNA and enrichment analysis", "row_count": 15, "column_count": 4}, "table": {"label": "Table 1", "caption": "The number and type of RNAs involved in each module.", "rows": [["Module color", "Number of RNAs", "Number of lncRNAs", "Number of mRNAs"], ["black", "124", "11", "113"], ["blue", "217", "5", "212"], ["brown", "215", "1", "214"], ["green", "206", "3", "203"], ["greenyellow", "88", "6", "82"], ["grey", "379", "17", "362"], ["magenta", "110", "3", "107"], ["pink", "122", "1", "121"], ["purple", "91", "2", "89"], ["red", "182", "15", "167"], ["salmon", "71", "6", "65"], ["tan", "80", "6", "74"], ["turquoise", "394", "8", "386"], ["yellow", "210", "19", "191"]], "row_count": 15, "column_count": 4, "numeric_cells": 42, "header_rows": 1, "locator": "section[10]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:31223533:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:766419648ca609ac3eaec91c2314f90b5c491f5f8e9cf557c10ad407a9894cd7", "bytes": 2958, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#table-2", "version": null, "note": "The Gene Ontology (GO) terms (A) and pathways (B) separately enriched for the mRNAs in RNA set1 and RNA set2.", "structure": {"pmcid": "PMC6571000", "section_index": 10, "section_title": "WGCNA and enrichment analysis", "row_count": 39, "column_count": 5}, "table": {"label": "Table 2", "caption": "The Gene Ontology (GO) terms (A) and pathways (B) separately enriched for the mRNAs in RNA set1 and RNA set2.", "rows": [["(A)"], ["Category", "Term", "Count", "P-value", "FDR"], ["RNA set1", "GO:0006350∼transcription", "155", "8.10E-12", "1.81E-08"], ["", "GO:0046649∼lymphocyte activation", "34", "2.86E-11", "3.20E-08"], ["", "GO:0045449∼regulation of transcription", "178", "7.42E-11", "5.54E-08"], ["", "GO:0045321∼leukocyte activation", "34", "5.22E-09", "2.92E-06"], ["", "GO:0030098∼lymphocyte differentiation", "21", "1.52E-08", "6.81E-06"], ["", "GO:0042110∼T cell activation", "23", "2.25E-08", "8.41E-06"], ["", "GO:0001775∼cell activation", "35", "1.07E-07", "3.42E-05"], ["", "GO:0030217∼T cell differentiation", "15", "5.89E-07", "1.65E-04"], ["", "GO:0002521∼leukocyte differentiation", "21", "9.30E-07", "2.31E-04"], ["", "GO:0030097∼hemopoiesis", "27", "1.27E-05", "2.84E-03"], ["", "GO:0006355∼regulation of transcription, DNA-dependent", "113", "2.25E-05", "4.57E-03"], ["", "GO:0048534∼hemopoietic or lymphoid organ development", "28", "2.54E-05", "4.73E-03"], ["", "GO:0002520∼immune system development", "29", "2.77E-05", "4.76E-03"], ["", "GO:0006955∼immune response", "54", "3.95E-05", "5.89E-03"], ["", "GO:0051252∼regulation of RNA metabolic process", "114", "3.70E-05", "5.91E-03"], ["", "GO:0042113∼B cell activation", "13", "1.00E-04", "1.39E-02"], ["", "GO:0002684∼positive regulation of immune system process", "24", "2.89E-04", "3.73E-02"], ["RNA set2", "GO:0006952∼defense response", "68", "5.40E-17", "1.32E-13"], ["", "GO:0009611∼response to wounding", "55", "1.48E-12", "1.81E-09"], ["", "GO:0009617∼response to bacterium", "29", "1.73E-10", "1.40E-07"], ["", "GO:0006954∼inflammatory response", "36", "3.71E-09", "2.26E-06"], ["", "GO:0006955∼immune response", "57", "3.78E-09", "1.84E-06"], ["", "GO:0001817∼regulation of cytokine production", "24", "9.50E-08", "3.86E-05"], ["", "GO:0042742∼defense response to bacterium", "18", "3.59E-07", "1.25E-04"], ["", "GO:0006935∼chemotaxis", "21", "8.54E-07", "2.60E-04"], ["", "GO:0042330∼taxis", "21", "8.54E-07", "2.60E-04"], ["", "GO:0007599∼hemostasis", "16", "5.45E-06", "1.47E-03"], ["", "GO:0002237∼response to molecule of bacterial origin", "14", "8.97E-06", "2.18E-03"], ["", "GO:0050817∼coagulation", "15", "1.28E-05", "2.84E-03"], ["", "GO:0007596∼blood coagulation", "15", "1.28E-05", "2.84E-03"], ["", "GO:0042060∼wound healing", "21", "1.33E-05", "2.69E-03"], ["", "GO:0006690∼icosanoid metabolic process", "10", "3.17E-05", "5.93E-03"], ["", "GO:0050878∼regulation of body fluid levels", "17", "3.61E-05", "6.26E-03"], ["", "GO:0033559∼unsaturated fatty acid metabolic process", "10", "6.25E-05", "1.01E-02"], ["", "GO:0032496∼response to lipopolysaccharide", "12", "7.47E-05", "1.13E-02"], ["", "GO:0045087∼innate immune response", "16", "1.03E-04", "1.47E-02"], ["", "GO:0007626∼locomotory behavior", "23", "2.79E-04", "3.51E-02"]], "row_count": 39, "column_count": 5, "numeric_cells": 148, "header_rows": 2, "locator": "section[10]/table-wrap[2]#table-2"}}, {"id": "asset:table:pmid:31223533:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4620ec04a41a42a78edfa074e5748957688d55640e29606e7b4ccf3ab8b4ef30", "bytes": 1515, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#table-3", "version": null, "note": "The pathways enriched for the mRNAs in the co-expression networks for RNA set1 and RNA set2.", "structure": {"pmcid": "PMC6571000", "section_index": 11, "section_title": "Co-expression network analysis", "row_count": 22, "column_count": 4}, "table": {"label": "Table 3", "caption": "The pathways enriched for the mRNAs in the co-expression networks for RNA set1 and RNA set2.", "rows": [["Category", "Term", "Count", "P-value"], ["RNA set1", "hsa04640:Hematopoietic cell lineage", "15", "2.25E-06"], ["", "hsa05340:Primary immunodeficiency", "9", "2.89E-05"], ["", "hsa04660:T cell receptor signaling pathway", "15", "3.41E-05"], ["", "hsa04662:B cell receptor signaling pathway", "10", "1.60E-03"], ["", "hsa03010:Ribosome", "9", "1.41E-02"], ["", "hsa04514:Cell adhesion molecules (CAMs)", "9", "1.12E-02"], ["", "hsa04650:Natural killer cell mediated cytotoxicity", "9", "1.15E-02"], ["", "hsa05330:Allograft rejection", "4", "1.45E-02"], ["", "hsa00600:Sphingolipid metabolism", "4", "1.72E-02"], ["", "hsa04350:TGF-beta signaling pathway", "6", "2.15E-02"], ["RNA set2", "hsa00480:Glutathione metabolism", "7", "3.50E-03"], ["", "hsa04060:Cytokine-cytokine receptor interaction", "17", "4.80E-03"], ["", "hsa00600:Sphingolipid metabolism", "6", "5.70E-03"], ["", "hsa00052:Galactose metabolism", "5", "6.90E-03"], ["", "hsa04142:Lysosome", "10", "7.90E-03"], ["", "hsa04621:NOD-like receptor signaling pathway", "7", "1.00E-02"], ["", "hsa04640:Hematopoietic cell lineage", "8", "1.39E-02"], ["", "hsa00010:Glycolysis/Gluconeogenesis", "6", "3.26E-02"], ["", "hsa00500:Starch and sucrose metabolism", "5", "3.56E-02"], ["", "hsa00030:Pentose phosphate pathway", "4", "3.72E-02"], ["", "hsa00561:Glycerolipid metabolism", "5", "4.43E-01"]], "row_count": 22, "column_count": 4, "numeric_cells": 63, "header_rows": 1, "locator": "section[11]/table-wrap[1]#table-3"}}], "gaps": []}, "analysis": {"state": "complete", "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": "Using the R package limma (version 3.34.0, https://bioconductor.org/packages/release/bioc/html/limma.html) (Ritchie et al., 2015), differential expression analysis for the two groups were carried out."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The following information was supplied regarding data availability:Raw data is available at EBI Array Express database under accession number E-MTAB-5195 here: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5195/."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:31223533", "asset:table:pmid:31223533:1", "asset:table:pmid:31223533:2", "asset:table:pmid:31223533:3", "asset:table:pmid:31223533:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:46:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28870, "completion_tokens": 1413, "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:31223533", "type": "paper", "label": "pmid:31223533"}, {"id": "source:pmid:31223533", "type": "manuscript", "label": "PMID 31223533 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31223533", "type": "paper", "label": "pmid:31223533"}, {"id": "source:pmid:31223533", "type": "manuscript", "label": "PMID 31223533 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31223533", "type": "extraction", "used": ["source:pmid:31223533"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:31223533", "parent_hash": "sha256:17245ea8d73a18c73ca1dbbcfffce304227aa4bb5fcef8c6d5d4782d133e5de9", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"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": ["Using the R package limma (version 3.34.0, https://bioconductor.org/packages/release/bioc/html/limma.html) (Ritchie et al., 2015), differential expression analysis for the two groups were carried out."], "order_basis": "analysis_only", "id": "assay:1"}]}