Analysis of protein-protein interaction network and functional modules on primary osteoporosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24656062", "kind": "science-record", "revision": 6, "content_hash": "sha256:8d6c8e49925f4513e9177b705e4f25930393617a2a60dcb81ec193105cc0c55f", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T21:58:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of protein-protein interaction network and functional modules on primary osteoporosis.", "doi": "10.1186/2047-783X-19-15", "pmid": "24656062", "authors": ["Gai-Li Li", "Xian-Hua Xu", "Bing-Ang Wang", "Yi-Min Yao", "Yang Qin", "Shu-Rong Bai", "Jian Rong", "Tao Deng", "Yong-He Hu"], "journal": "European journal of medical research", "year": 2014, "abstract": "BACKGROUND: Primary osteoporosis is an age-related disease, and the main cause of this disease is the failure of bone homeostasis. Previous studies have shown that primary osteoporosis is associated with gene mutations.To explore the functional modules of the PPI (protein-protein interaction) network of differentially expressed genes (DEGs), and the related pathways participating in primary osteoporosis.\nMETHODS: The gene expression profile of primary osteoporosis GSE35956 was downloaded from the GEO (Gene Expression Omnibus) database and included five MSC (mesenchymal stem cell) specimens of normal osseous tissue and five MSC specimens of osteoporosis. The DEGs between the two types of MSC specimens were identified by the samr package in R language. In addition, the functions and pathways of DEGs were enriched. Then the DEGs were mapped to String to acquire PPI pairs and the PPI network was constructed with by these PPI pairs. Topological properties of the network were calculated by Network Analyzer, and modules in the network were screened by Cluster ONE software. Subsequently, the fronting five modules whose P-value was less than 1.0e-05 were identified and function analysis was conducted.\nRESULTS: A total of 797 genes were filtered as DEGs from these ten specimens of GSE35956 with 660 up-regulated genes and 137 down-regulated genes. Meanwhile, up-regulated DEGs were mainly enriched in functions and pathways related to cell cycle and DNA replication. Furthermore, there were 4,135 PPI pairs and 377 nodes in the PPI network. Four modules were enriched in different pathways, including cell cycle and DNA replication pathway in module 2.\nCONCLUSIONS: In this paper, we explored the genes and pathways involved in primary osteoporosis based on gene expression profiles, and the present findings have the potential to be used clinically for the future treatment of primary osteoporosis.", "claims": [{"id": "claim-method", "statement": "The DEGs between MSC specimens of normal osseous tissue and MSC specimens of osteoporosis were identified by the samr package in R software [14]. The cut-off criteria were delta = 1, fold change ≥ 2 and FDR (false discovery rate) was less than 0.05. The gene expression profile of GSE35956 [11] was downloaded from a public functional genomics data repository GEO (Gene Expression Omnibus) database which is based on the GPL570 [HG-U133 Plus 2] Affymetrix Human Genome U133 Plus 2.0 Array platform (Affymetrix, Santa Clara city, CA state, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24656062", "locator": "sections[5] \"Screening of DEGs\" paragraph 2", "quote": "The DEGs between MSC specimens of normal osseous tissue and MSC specimens of osteoporosis were identified by the samr package in R software [14]."}, {"asset": "source:pmid:24656062", "locator": "sections[5] \"Screening of DEGs\" paragraph 2", "quote": "The cut-off criteria were delta = 1, fold change ≥ 2 and FDR (false discovery rate) was less than 0.05."}, {"asset": "source:pmid:24656062", "locator": "sections[3] \"Derivation of genetic data\" paragraph 2", "quote": "The gene expression profile of GSE35956 [11] was downloaded from a public functional genomics data repository GEO (Gene Expression Omnibus) database which is based on the GPL570 [HG-U133 Plus 2] Affymetrix Human Genome U133 Plus 2.0 Array platform (Affymetrix, Santa Clara city, CA state, USA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile of GSE35956 [11] was downloaded from a public functional genomics data repository GEO (Gene Expression Omnibus) database which is based on the GPL570 [HG-U133 Plus 2] Affymetrix Human Genome U133 Plus 2.0 Array platform (Affymetrix, Santa Clara city, CA state, USA). A total of ten specimens, including five MSC specimens of normal osseous tissue and five MSC specimens of osteoporosis, were available for further study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24656062", "locator": "sections[3] \"Derivation of genetic data\" paragraph 2", "quote": "The gene expression profile of GSE35956 [11] was downloaded from a public functional genomics data repository GEO (Gene Expression Omnibus) database which is based on the GPL570 [HG-U133 Plus 2] Affymetrix Human Genome U133 Plus 2.0 Array platform (Affymetrix, Santa Clara city, CA state, USA). A total of ten specimens, including five MSC specimens of normal osseous tissue and five MSC specimens of osteoporosis, were available for further study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the samr package in R on the GSE35956 gene-expression profile downloaded from GEO, the study identified 797 differentially expressed genes between normal and osteoporotic mesenchymal stem-cell specimens.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24656062", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The gene expression profile of primary osteoporosis GSE35956 was downloaded from the GEO (Gene Expression Omnibus) database and included five MSC (mesenchymal stem cell) specimens of normal osseous tissue and five MSC specimens of osteoporosis."}, {"asset": "source:pmid:24656062", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The DEGs between the two types of MSC specimens were identified by the samr package in R language."}, {"asset": "source:pmid:24656062", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "A total of 797 genes were filtered as DEGs from these ten specimens of GSE35956 with 660 up-regulated genes and 137 down-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the samr package in R on the GSE35956 gene-expression profile downloaded from GEO, the study identified 797 differentially expressed genes between normal and osteoporotic mesenchymal stem-cell specimens.", "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:24656062"], "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:GSE35956"], "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:GSE35956"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24656062", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/2047-783X-19-15", "sha256": "sha256:0d87d6c94e0e37dc097d72756702fd593267262bee7948309277f60c1e3dda0c", "bytes": 19520, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/2047-783X-19-15", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3994448", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE35956", "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=GSE35956", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35956", "version": null, "note": "The gene expression profile of GSE35956 [11] was downloaded from a public functional genomics data repository GEO (Gene Expression Omnibus) database which is based on the GPL570 [HG-U133 Plus 2] Affymetrix Human Genome U133 Plus 2.0 Array platform (Affymetrix, Santa Clara city, CA state, USA). 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The cut-off criteria were delta = 1, fold change ≥ 2 and FDR (false discovery rate) was less than 0.05. The gene expression profile of GSE35956 [11] was downloaded from a public functional genomics data repository GEO (Gene Expression Omnibus) database which is based on the GPL570 [HG-U133 Plus 2] Affymetrix Human Genome U133 Plus 2.0 Array platform (Affymetrix, Santa Clara city, CA state, USA)."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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