Bioinformatics-Based Identification of Potential Hypoxia-Related Genes Associated With Peyronie's Disease.

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This study applied bioinformatic approaches to select candidate hypoxia-related genes involved in the pathogenesis of PD. The Gene Expression Omnibus (GEO) data set GSE146500 was introduced to compare the transcriptional profiling between normal and PD samples. The differential expression of hypoxia-related gene was determined with R software. On the selected candidate genes, further functional analyses were applied, including protein-protein interactions (PPIs), gene correlation, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. A total of 66 candidate genes (24 candidates overexpressed in PD and 42 showing reduced expression in PD) were distinguished according to the differential expression between human fibroblast cells from normal and PD patients. The interactions among these candidate genes were recognized according to PPI analysis. The functional enrichment analyses revealed the potential modulatory functions of the candidate genes in some major biological processes, especially in glycolysis/gluconeogenesis and carbon metabolism. The findings would facilitate further study on the pathogenesis of PD, which might consequently promote the improvement of clinical strategies against PD.", "claims": [{"id": "claim-method", "statement": "The “limma” package of R software was used to identify candidate hypoxia-related genes with differential expression levels in PD. The changes in expression levels with adjusted absolute fold-change > 1 and p < .05 were considered as significant differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35894424", "locator": "sections[4] \"Differential Expression Analysis of Hypoxia-Related Genes\" paragraph 2", "quote": "The “limma” package of R software was used to identify candidate hypoxia-related genes with differential expression levels in PD. The changes in expression levels with adjusted absolute fold-change > 1 and p < .05 were considered as significant differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Through the GEO website (http://www.ncbi.nlm.nih.gov/geo/), the data set GSE146500 was obtained, which contained the comprehensive transcriptional profiles of normal and PD patient samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35894424", "locator": "sections[3] \"Microarray Data and the Selection of Hypoxia-Related Genes\" paragraph 2", "quote": "Through the GEO website (http://www.ncbi.nlm.nih.gov/geo/), the data set GSE146500 was obtained, which contained the comprehensive transcriptional profiles of normal and PD patient samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Sixty-six hypoxia-related genes were differentially expressed in PD, including 42 showing reduced expression and 24 showing overexpression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35894424", "locator": "sections[9] \"Retrospective Identification of Hypoxia-Related Genes Differentially Expressed in PD\" paragraph 2", "quote": "According to our selection criteria (absolute fold-change > 1, adjusted p < .05), 66 hypoxia-related genes with differential expression in PD were distinguished, including 42 genes showing reduced expression and 24 showing overexpression in PD (Figure 1C)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Sixty-six hypoxia-related genes were differentially expressed in PD, including 42 showing reduced expression and 24 showing overexpression.", "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:35894424"], "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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