Identifying Key Genes and Functionally Enriched Pathways of Diverse Adipose Tissue Types in Cattle.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35237299", "kind": "science-record", "revision": 5, "content_hash": "sha256:c72cc459d0e152f342f033c6abfd8d8bdba61c24cd16c19087dbcfb6c7843491", "created_at": "2026-11-01T17:36:59Z", "updated_at": "2026-11-01T22:06:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying Key Genes and Functionally Enriched Pathways of Diverse Adipose Tissue Types in Cattle.", "doi": "10.3389/fgene.2022.790690", "pmid": "35237299", "authors": ["Cuili Pan", "Chaoyun Yang", "Shuzhe Wang", "Yun Ma"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: Fat is a tissue that not just stores energy and plays a protective role; it is also a vital endocrine organ that generates and integrates signals to influence metabolism. Meanwhile, the excessive accumulation of lipids in adipose tissue can lead to metabolic disturbance and diseases. To date, the complicated molecular mechanisms of bovine adipose tissue are still unknown. This study aimed to identify key genes and functionally enriched pathways in various adipose tissue types. Results: The RNAseq data of 264 samples were downloaded from Gene Expression Omnibus (GEO) and analyzed by weighted gene co-expression network analysis (WGCNA). We identified 19 modules that significantly associated with at least one adipose tissue type. The brown module from GSE39618 was most closely associated with intramuscular fat tissue, which contained 550 genes. These genes were significantly enriched in pathways that related to inflammation and disease, such as TNF signaling pathway, IL-17 signaling pathway, and NF-kappa B signaling pathway. The pink module (GSE39618) that contained 58 genes was most closely associated with omental fat tissue. The turquoise (GSE39618), blue (GSE116775), and yellow (GSE65125) module were most closely associated with subcutaneous fat tissue. Genes in these modules were significantly enriched in pathways related to fat metabolism, such as the PPAR signaling pathway, fatty acid metabolism and PI3K-Akt signaling pathway. At last, key genes for intramuscular fat (PTGS2 and IL6), omental fat (ARHGEF5 and WT1), and subcutaneous fat (KIT, QR6Q1, PKD2L1, etc.) were obtained and verified. In addition, it was found that IL10 and VCAM1 might be potential genes to distinguish adipose and muscle. Conclusion: The study applied WGCNA to generate a landscape of adipose tissue and provide a basis for identifying potential pathways and hub genes of different adipose tissue types.", "claims": [{"id": "claim-method", "statement": "The RNAseq data of 264 samples were downloaded from Gene Expression Omnibus (GEO) and analyzed by weighted gene co-expression network analysis (WGCNA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35237299", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The RNAseq data of 264 samples were downloaded from Gene Expression Omnibus (GEO) and analyzed by weighted gene co-expression network analysis (WGCNA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets used in the study are stored in the Gene Expression Omnibus (GEO) database. Below are the direct links (GSE39618:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE39618; GSE116775:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE116775; GSE65125:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE65125).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35237299", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets used in the study are stored in the Gene Expression Omnibus (GEO) database. Below are the direct links (GSE39618:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE39618; GSE116775:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE116775; GSE65125:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE65125)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 19 modules that significantly associated with at least one adipose tissue type.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35237299", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We identified 19 modules that significantly associated with at least one adipose tissue type."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 19 modules that significantly associated with at least one adipose tissue type.", "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:35237299"], "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:GSE116775"], "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:GSE116775"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35237299", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.790690", "sha256": "sha256:91d7ed966829c789f7adf7f3d04a3c52be1e84b27e92f9add6099e58df9ca954", "bytes": 40374, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.790690", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8884536", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116775", "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=GSE116775", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116775", "version": null, "note": "Publicly available datasets were analyzed in this study. 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This data can be found here: The datasets used in the study are stored in the Gene Expression Omnibus (GEO) database. Below are the direct links (GSE39618:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE39618; GSE116775:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE116775; GSE65125:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE65125).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets used in the study are stored in the Gene Expression Omnibus (GEO) database. 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This data can be found here: The datasets used in the study are stored in the Gene Expression Omnibus (GEO) database. Below are the direct links (GSE39618:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE39618; GSE116775:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE116775; GSE65125:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE65125).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: The datasets used in the study are stored in the Gene Expression Omnibus (GEO) database. Below are the direct links (GSE39618:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE39618; GSE116775:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE116775; GSE65125:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE65125).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1587661", "GSM1587662", "GSM1587663", "GSM1587664", "GSM1587665", "GSM1587666", "GSM1587667", "GSM1587668", "GSM1587669", "GSM1587670", "GSM1587671", "GSM1587672", "GSM1587673", "GSM1587674", "GSM1587675", "GSM1587676", "GSM1587677", "GSM1587678", "GSM1587679", "GSM1587680", "GSM1587681", "GSM1587682", "GSM1587683", "GSM1587684", "GSM1587685", "GSM1587686", "GSM1587687", "GSM1587688", "GSM1587689", "GSM1587690", "GSM1587691", "GSM1587692", "GSM1587693", "GSM1587694", "GSM1587695", "GSM1587696", "GSM1587697", "GSM1587698", "GSM1587699", "GSM1587700"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "15749", "taxon": "Bos taurus", "title": "Comprehensive identification of sexually dimorphic genes using RNA-seq with several tissues of cattle", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116775 not downloaded", "asset:data:geo:GSE116775 licence not read", "asset:data:geo:GSE39618 not downloaded", "asset:data:geo:GSE39618 licence not read", "asset:data:geo:GSE65125 not downloaded", "asset:data:geo:GSE65125 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-2", "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"}}, {"id": "method-3", "family": null, "specific": null, "label": "weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The RNAseq data of 264 samples were downloaded from Gene Expression Omnibus (GEO) and analyzed by weighted gene co-expression network analysis (WGCNA)."}}], "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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