The Identification of RPL4 as a Hub Gene Associated with Goat Litter Size via Weighted Gene Co-Expression Network Analysis.

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In recent years, researchers have identified numerous genes associated with goat reproductive performance through high-throughput sequencing, single-cell sequencing, gene knockout, and other techniques. However, there is still an urgent need to explore marker genes related to goat reproductive performance. In this study, a single-cell RNA sequencing dataset of oocytes (GSE136005) was obtained from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-expression Network Analysis (WGCNA) was utilized to identify modules highly correlated with goat litter size. Through gene function enrichment analysis, it was found that genes within the modules were mainly enriched in adhesive junctions, cell cycle, and other signaling pathways. Additionally, the top 30 hub genes with the highest connectivity in WGCNA were identified. Subsequently, using Protein-Protein Interaction (PPI) network analysis, the top 30 genes with the highest connectivity within the modules were identified. The intersection of hub genes, key genes in the PPI network, and differentially expressed genes (DEGs) led to the identification of the RPL4 gene as a key marker gene associated with reproductive capacity in goat oocytes. Overall, our study reveals that the RPL4 gene in oocytes holds promise as a biological marker for assessing goat litter size, deepening our understanding of the regulatory mechanisms underlying goat reproductive performance.", "claims": [{"id": "claim-method", "statement": "Weighted Gene Co-expression Network Analysis (WGCNA) was utilized to identify modules highly correlated with goat litter size.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38791687", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Weighted Gene Co-expression Network Analysis (WGCNA) was utilized to identify modules highly correlated with goat litter size."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data from this study were deposited in the GEO database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 10 December 2023) under the accession number PRJNA560927.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38791687", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The data from this study were deposited in the GEO database (https://www.ncbi.nlm.nih.gov/geo/, accessed on 10 December 2023) under the accession number PRJNA560927."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study identified the RPL4 gene as a key marker gene related to reproductive capacity in goat oocytes through various bioinformatics analysis methods including WGCNA, PPI network analysis, and differential gene expression analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38791687", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study identified the RPL4 gene as a key marker gene related to reproductive capacity in goat oocytes through various bioinformatics analysis methods including WGCNA, PPI network analysis, and differential gene expression analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study identified the RPL4 gene as a key marker gene related to reproductive capacity in goat oocytes through various bioinformatics analysis methods including WGCNA, PPI network analysis, and differential gene expression analysis.", "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:38791687"], "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. 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