Analysis of the different characteristics between omental preadipocytes and differentiated white adipocytes using bioinformatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35499169", "kind": "science-record", "revision": 5, "content_hash": "sha256:013a52f96be3382c5e0453481f37857e0b39c298ab5176e35cdb4b89116f2f69", "created_at": "2026-11-01T18:14:23Z", "updated_at": "2026-11-01T22:48:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of the different characteristics between omental preadipocytes and differentiated white adipocytes using bioinformatics methods.", "doi": "10.1080/21623945.2022.2063471", "pmid": "35499169", "authors": ["Xinyu Yang", "Lu Li", "Canming Xu", "Meichen Pi", "Changhua Wang", "Yemin Zhang"], "journal": "Adipocyte", "year": 2022, "abstract": "Obesity is emerging as an epidemiological issue, being associated with the onset and progress of various metabolism-related disorders. Obesity is characterized by the white adipose expansion, which encounters white adipocyte hypertrophy and hyperplasia. White adipocyte hyperplasia is defined as adipogenesis with the increase in the number of the white adipocytes from the preadipocytes. Adipogenesis contributes to distributing excess triglycerides among the smaller newly formed adipocytes, reducing the number of hypertrophic adipocytes and secreting anti-inflammatory factor. Therefore, adipogenesis is emerging as a new therapeutic target for the treatment of obesity. In the present study, for a better understanding of the contribution of the alteration of the omental differentiated white adipocytes to the systemic metabolic disorders, we downloaded the mRNA expression profiles from GEO database GSE1657, 328 differentially expressed genes (DEGs) were screened between the undifferentiated preadipocytes (UNDIF) and omental differentiated white adipocytes (DIF). The contributions of the upregulated and downregulated DEGs to the system were performed via the Gene Ontology (GO) analysis, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Protein-Protein Interaction (PPI) network, respectively. The potential contribution of the whole altered genes in the differentiated white adipocytes was explored with the performance of Gene Set Enrichment Analysis (GSEA), especially on the GO analysis, KEGG analysis, hallmark analysis, oncogenic analysis and related miRNA analysis. The output of the current study will shed light on the new targets for the treatment of obesity and obesity-related disorders.", "claims": [{"id": "claim-method", "statement": "Following the databases annotated by the performance of Perl script, the limma package in R software (version 3.6.3) (University of California, Berkeley, CA) was applied to screen the DEGs with the threshold criterion of adjusted p < 0.05 and |log2 FC|; (foldchange) >1 between the UNDIF and DIF white adipocytes group [12].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35499169", "locator": "sections[5] \"Microarray data and DEGs identification\" paragraph 2", "quote": "Following the databases annotated by the performance of Perl script, the limma package in R software (version 3.6.3) (University of California, Berkeley, CA) was applied to screen the DEGs with the threshold criterion of adjusted p < 0.05 and |log2 FC|; (foldchange) >1 between the UNDIF and DIF white adipocytes group [12]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study are available on request to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35499169", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The datasets generated for this study are available on request to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After consolidation and normalization of the microarray data, 328 DEGs between UNDIF and DIF omental white adipocytes groups were screened by the limma package (|Log2FC| >1, adjusted p < 0.05), as shown in the heatmap (Figure 1).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "After consolidation and normalization of the microarray data, 328 DEGs between UNDIF and DIF omental white adipocytes groups were screened by the limma package (|Log2FC| >1, adjusted p < 0.05), as shown in the heatmap (Figure 1)."}, "evidence": [{"asset": "source:pmid:35499169", "locator": "sections[11] \"Identification of DEGs related to omental WAT differentiation\" paragraph 2", "quote": "After consolidation and normalization of the microarray data, 328 DEGs between UNDIF and DIF omental white adipocytes groups were screened by the limma package (|Log2FC| >1, adjusted p < 0.05), as shown in the heatmap (Figure 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After consolidation and normalization of the microarray data, 328 DEGs between UNDIF and DIF omental white adipocytes groups were screened by the limma package (|Log2FC| >1, adjusted p < 0.05), as shown in the heatmap (Figure 1).", "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:35499169"], "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:GSE1657"], "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:GSE1657"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35499169", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/21623945.2022.2063471", "sha256": "sha256:195f577d33a8ffe01e3781e02be06ad1c5af1d381b3dd36cb0a0da0e91f09311", "bytes": 30130, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/21623945.2022.2063471", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9067510", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1657", "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=GSE1657", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1657", "version": null, "note": "The datasets generated for this study are available on request to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study are available on request to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM28475", "GSM28476", "GSM28477", "GSM28478", "GSM28479", "GSM28480", "GSM28481", "GSM28482", "GSM28483", "GSM28484", "GSM28485", "GSM28486", "GSM28487", "GSM28488", "GSM28489", "GSM28490", "GSM28491", "GSM28492", "GSM28493", "GSM28494", "GSM28495", "GSM28496", "GSM28497", "GSM28498", "GSM30645", "GSM30646", "GSM30647", "GSM30648", "GSM30649", "GSM30650", "GSM30651", "GSM30652", "GSM30653", "GSM30654", "GSM30655", "GSM30656", "GSM30657", "GSM30658", "GSM30659", "GSM30660", "GSM30661", "GSM30662"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97", "taxon": "Homo sapiens", "title": "Adipocyte Differentiation", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE1657 not downloaded", "asset:data:geo:GSE1657 licence not read"]}, "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": "Following the databases annotated by the performance of Perl script, the limma package in R software (version 3.6.3) (University of California, Berkeley, CA) was applied to screen the DEGs with the threshold criterion of adjusted p < 0.05 and |log2 FC|; (foldchange) >1 between the UNDIF and DIF white adipocytes group [12]."}}, {"id": "method-2", "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"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. 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