Identification of the core genes in Randall's plaque of kidney stone and immune infiltration with WGCNA network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36816033", "kind": "science-record", "revision": 4, "content_hash": "sha256:e703483b6578a1dd7cb869128de2c6ee0bd3a70d0064f49f1938f5eb40c702ba", "created_at": "2026-11-01T19:01:24Z", "updated_at": "2026-11-01T22:51:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the core genes in Randall's plaque of kidney stone and immune infiltration with WGCNA network.", "doi": "10.3389/fgene.2023.1048919", "pmid": "36816033", "authors": ["Lingyun Yu", "Gefei Li", "Shiyao Jin", "Jiahong Su", "Shoulin Li"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: Randall's plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease. Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein-protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518. Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518. Conclusion: Randall's plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.", "claims": [{"id": "claim-method", "statement": "In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36816033", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36816033", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 840 upregulated and 1065 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36816033", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The study identified 840 upregulated and 1065 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 840 upregulated and 1065 downregulated genes.", "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:36816033"], "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:GSE117518"], "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:GSE117518"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36816033", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1048919", "sha256": "sha256:8619add88cad1359d04a1455ec1e5f954fca52fdc84590b5268ca0f8d6379870", "bytes": 38754, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2023.1048919", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9931196", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE117518", "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=GSE117518", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE117518", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3302157", "GSM3302158", "GSM3302159", "GSM3302160", "GSM3302161", "GSM3302162"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "21827", "taxon": "Homo sapiens", "title": "Microarray analysis of long noncoding RNA and mRNA expression profiles in Randall’s Plaques of CaOx stones patients", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE73680", "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=GSE73680", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73680", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1900673", "GSM1900674", "GSM1900675", "GSM1900676", "GSM1900677", "GSM1900678", "GSM1900679", "GSM1900680", "GSM1900681", "GSM1900682", "GSM1900683", "GSM1900684", "GSM1900685", "GSM1900686", "GSM1900687", "GSM1900688", "GSM1900689", "GSM1900690", "GSM1900691", "GSM1900692", "GSM1900693", "GSM1900694", "GSM1900695", "GSM1900696", "GSM1900697", "GSM1900698", "GSM1900699", "GSM1900700", "GSM1900701", "GSM1900702", "GSM1900703", "GSM1900704", "GSM1900705", "GSM1900706", "GSM1900707", "GSM1900708", "GSM1900709", "GSM1900710", "GSM1900711", "GSM1900712", "GSM1900713", "GSM1900714", "GSM1900715", "GSM1900716", "GSM1900717", "GSM1900718", "GSM1900719", "GSM1900720", "GSM1900721", "GSM1900722", "GSM1900723", "GSM1900724", "GSM1900725", "GSM1900726", "GSM1900727", "GSM1900728", "GSM1900729", "GSM1900730", "GSM1900731", "GSM1900732", "GSM1900733", "GSM1900734"], "sample_count": 62, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Gene expression profile of Randall's Plaque tissue", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE117518 not downloaded", "asset:data:geo:GSE117518 licence not read", "asset:data:geo:GSE73680 not downloaded", "asset:data:geo:GSE73680 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "principal component analysis"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE73680", "GSE117518"], "resolved_accessions": ["GSE73680", "GSE117518"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE73680, GSE117518 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36816033", "data:geo:GSE117518"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE117518"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:28:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12446, "completion_tokens": 2061, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36816033", "type": "paper", "label": "pmid:36816033"}, {"id": "source:pmid:36816033", "type": "manuscript", "label": "PMID 36816033 full text"}, {"id": "data:geo:GSE117518", "type": "dataset", "label": "GEO GSE117518"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36816033", "type": "paper", "label": "pmid:36816033"}, {"id": "source:pmid:36816033", "type": "manuscript", "label": "PMID 36816033 full text"}, {"id": "data:geo:GSE117518", "type": "dataset", "label": "GEO GSE117518"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36816033", "type": "extraction", "used": ["source:pmid:36816033"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE117518", "type": "accession_resolution", "used": ["data:geo:GSE117518"], "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:36816033", "parent_hash": "sha256:6c5a5bbface955e945458d2067540fa8f671267a1bd21c1614f8a816764a77d7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE117518 licence not read", "asset:data:geo:GSE117518 not downloaded", "asset:data:geo:GSE73680 licence not read", "asset:data:geo:GSE73680 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package."], "order_basis": "analysis_only", "id": "assay:1"}]}