Comparative transcriptomic study on the ovarian cancer between chicken and human.

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We performed next-generation sequencing of microRNA and mRNA expression profiles in 9 chicken ovarian cancers and 4 normal ovaries, which has been deposited in GSE246604. Together with 6 public datasets (GSE21706, GSE40376, GSE18520, GSE27651, GSE66957, TCGA-OV), we conducted a comparative transcriptomics study between chicken and human. In the present study, miR-451, miR-2188-5p, and miR-10b-5p were differentially expressed in normal ovaries, early- and late-stage ovarian cancers. We also disclosed 499 up-regulated genes and 1,061 down-regulated genes in chicken ovarian cancer. The molecular signals from 9 cancer hallmarks, 25 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 369 Gene Ontology (GO) pathways exhibited abnormalities in ovarian cancer compared to normal ovaries via Gene Set Enrichment Analysis (GSEA). In the comparative analysis across species, we have uncovered the conservation of 5 KEGG and 76 GO pathways between chicken and human including the mismatch repair and ECM receptor interaction pathways. Moreover, a total of 174 genes contributed to the core enrichment for these KEGG and GO pathways were identified. Among these genes, the 22 genes were found to be associated with overall survival in patients with ovarian cancer. In general, we revealed the microRNA profiles of ovarian cancers in hens and updated the mRNA profiles previously derived from microarrays. And we also disclosed the molecular pathways and core genes of ovarian cancer shared between hens and women, which informs model animal studies and gene-targeted drug development.", "claims": [{"id": "claim-method", "statement": "Gene set enrichment analysis (GSEA) was a useful tool to investigate whether pathways were significantly enriched in neoplastic or normal states.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39002367", "locator": "sections[9] \"Bioinformatics Analysis\" paragraph 2", "quote": "Gene set enrichment analysis (GSEA) was a useful tool to investigate whether pathways were significantly enriched in neoplastic or normal states."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We performed next-generation sequencing of microRNA and mRNA expression profiles in 9 chicken ovarian cancers and 4 normal ovaries, which has been deposited in GSE246604.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39002367", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We performed next-generation sequencing of microRNA and mRNA expression profiles in 9 chicken ovarian cancers and 4 normal ovaries, which has been deposited in GSE246604."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Comparative transcriptomic analysis identified 5 KEGG pathways and 76 GO pathways conserved between chicken and human ovarian cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39002367", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In the comparative analysis across species, we have uncovered the conservation of 5 KEGG and 76 GO pathways between chicken and human including the mismatch repair and ECM receptor interaction pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Comparative transcriptomic analysis identified 5 KEGG pathways and 76 GO pathways conserved between chicken and human ovarian cancer.", "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:39002367"], "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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