Identification of key genes associated with Schmid-type metaphyseal chondrodysplasia based on microarray data.

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Microarray data from GSE72261 were downloaded from the NCBI GEO database, including collagen X p.Asn617Lys knock-in mutation (ColXN617K), ablated XBP1 activity (Xbp1CartΔEx2), compound mutant (C/X), and wild-type (WT) specimens. Differentially expressed genes (DEGs) were screened in Xbp1 vs. WT, Col vs. WT and CX vs. WT, respectively. Pathway enrichment analysis of these DEGs was performed. Transcription factors (TFs) of the overlapping DEGs were identified. Weighted correlation network analysis (WGCNA) was performed to find modules of DEGs with high correlations, followed by gene function analysis and a protein-protein interaction network construction. In total, 481, 1,530 and 1,214 DEGs were identified in Xbp1 vs. WT, Col vs. WT and CX vs. WT, respectively. These DEGs were enriched in different pathways, such as extracellular matrix (ECM)-receptor interaction and metabolism-related pathways. A total of 7 TFs were found to regulate 19 common upregulated genes, and 4 TFs were identified to regulate 21 common downregulated genes. Two significant gene co-expression modules were enriched and DEGs in the 2 modules were mainly enriched in different biological processes, such as ribosome biogenesis. Moreover, Kras (downregulated), Col5a1 (upregulated) and Furin (upregulated) were both identified in the regulatory networks and protein-protein interaction (PPI) network. On the whole, our findings indicate that the Kras, Col5a1 and Furin genes may play essential roles in the molecular mechanisms of SMCD, which warrants further investigation.", "claims": [{"id": "claim-method", "statement": "|log2fold change (FC)| and p-values from an unpaired t-test implemented in the limma package (15) were used to select the DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28440393", "locator": "sections[4] \"Screening of DEGs\" paragraph 2", "quote": "|log2fold change (FC)| and p-values from an unpaired t-test implemented in the limma package (15) were used to select the DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data of GSE72261, deposited by Cameron et al (11), were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (http://www.nibi.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28440393", "locator": "sections[3] \"Microarray data and data preprocessing\" paragraph 2", "quote": "The microarray data of GSE72261, deposited by Cameron et al (11), were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (http://www.nibi.nih.gov/geo/)."}], "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:28440393"], "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:GSE72261"], "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:GSE72261"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28440393", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ijmm.2017.2954", "sha256": 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(NCBI) Gene Expression Omnibus (GEO) database (http://www.nibi.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of GSE72261, deposited by Cameron et al (11), were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (http://www.nibi.nih.gov/geo/).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1858964", "GSM1858965", "GSM1858966", "GSM1858967", "GSM1858968", "GSM1858969", "GSM1858970", "GSM1858971", "GSM1858972", "GSM1858973", "GSM1858974", "GSM1858975"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "6887", "taxon": "Mus musculus", "title": "Analysis of the IRE1/XBP1 unfolded protein response (UPR) pathway in Schmid metaphyseal chondrodysplasia hypertrophic chondrocyte endoplasmic reticulum (ER) stress", "resolution_checked_at": "2026-11-01T15:39:55Z", 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Col group and CX group, respectively.", "rows": [["Gene change", "KEGG term", "Count", "p-value"], ["In Xbp1 group", "", "", ""], ["Upregulated", "mmu04512:ECM-receptor interaction", "8", "5.23E-04"], ["mmu04510:Focal adhesion", "11", "0.0020"], ["mmu04142:Lysosome", "8", "0.0043"], ["mmu00561:Glycerolipid metabolism", "4", "0.0468"], ["Downregulated", "mmu03010:Ribosome", "8", "2.69E-05"], ["mmu00860:Porphyrin and chlorophyll metabolism", "3", "0.0364"], ["In Col group", "", "", ""], ["Upregulated", "mmu00970:Aminoacyl-tRNA biosynthesis", "8", "0.0011"], ["mmu00051:Fructose and mannose metabolism", "7", "0.0030"], ["mmu00600:Sphingolipid metabolism", "7", "0.0057"], ["mmu00250:Alanine, aspartate and glutamate metabolism", "6", "0.00594"], ["mmu04142:Lysosome", "12", "0.0071"], ["mmu00290:Valine, leucine and isoleucine biosynthesis", "4", "0.00796"], ["mmu00510:N-Glycan biosynthesis", "7", "0.00893"], ["mmu03018:RNA degradation", "8", "0.00895"], ["mmu00480:Glutathione metabolism", 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water-soluble vitamin biosynthetic process", "4", "0.0071"], ["GO:0034470 - ncRNA processing", "9", "0.0083"], ["GO:0000041 - transition metal ion transport", "6", "0.0088"], ["GO:0055114 - oxidation reduction", "22", "0.0109"], ["GO:0034660 - ncRNA metabolic process", "10", "0.0116"], ["GO:0016053 - organic acid biosynthetic process", "8", "0.0146"], ["GO:0046394 - carboxylic acid biosynthetic process", "8", "0.0146"], ["Green", "GO:0007155 - cell adhesion", "14", "0.0126"], ["GO:0022610 - biological adhesion", "14", "0.0128"], ["GO:0006928 - cell motion", "10", "0.0258"], ["GO:0006695 - cholesterol biosynthetic process", "3", "0.0283"], ["GO:0055114 - oxidation reduction", "14", "0.0456"], ["GO:0016126 - sterol biosynthetic process", "3", "0.0462"], ["GO:0006865 - amino acid transport", "4", "0.0482"], ["GO:0006694 - steroid biosynthetic process", "4", "0.0482"]], "row_count": 19, "column_count": 4, "numeric_cells": 54, "header_rows": 1, "locator": 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