Identification of key genes and pathways in adrenocortical carcinoma: evidence from bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38053725", "kind": "science-record", "revision": 4, "content_hash": "sha256:8d7314a6d25266772c5617c8681d17b649580b5e2492527c6e8a0450ec7d83b7", "created_at": "2026-11-01T19:03:00Z", "updated_at": "2026-11-01T22:10:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes and pathways in adrenocortical carcinoma: evidence from bioinformatic analysis.", "doi": "10.3389/fendo.2023.1250033", "pmid": "38053725", "authors": ["Mengsha Yin", "Yao Wang", "Xinhua Ren", "Mingyue Han", "Shanshan Li", "Ruishuang Liang", "Guixia Wang", "Xiaokun Gang"], "journal": "Frontiers in endocrinology", "year": 2023, "abstract": "Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with poor prognosis. The disease originates from the cortex of adrenal gland and lacks effective treatment. Efforts have been made to elucidate the pathogenesis of ACC, but the molecular mechanisms remain elusive. To identify key genes and pathways in ACC, the expression profiles of GSE12368, GSE90713 and GSE143383 were downloaded from the Gene Expression Omnibus (GEO) database. After screening differentially expressed genes (DEGs) in each microarray dataset on the basis of cut-off, we identified 206 DEGs, consisting of 72 up-regulated and 134 down-regulated genes in three datasets. Function enrichment analyses of DEGs were performed by DAVID online database and the results revealed that the DEGs were mainly enriched in cell cycle, cell cycle process, mitotic cell cycle, response to oxygen-containing compound, progesterone-mediated oocyte maturation, p53 signaling pathway. The STRING database was used to construct the protein-protein interaction (PPI) network, and modules analysis was performed using Cytoscape. Finally, we filtered out eight hub genes, including CDK1, CCNA2, CCNB1, TOP2A, MAD2L1, BIRC5, BUB1 and AURKA. Biological process analysis showed that these hub genes were significantly enriched in nuclear division, mitosis, M phase of mitotic cell cycle and cell cycle process. Violin plot, Kaplan-Meier curve and stage plot of these hub genes confirmed the reliability of the results. In conclusion, the results in this study provided reliable key genes and pathways for ACC, which will be useful for ACC mechanisms, diagnosis and candidate targeted treatment.", "claims": [{"id": "claim-method", "statement": "The DEGs between ACC and normal samples in each GEO dataset were screened using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38053725", "locator": "sections[4] \"Data preprocessing and identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "The DEGs between ACC and normal samples in each GEO dataset were screened using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The data that support the findings of this study are available in the GEO database (http://www.ncbi.nlm.nih.gov/geo) under reference numbers [GSE12368, GSE90713, GSE143383].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38053725", "locator": "sections[15] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The data that support the findings of this study are available in the GEO database (http://www.ncbi.nlm.nih.gov/geo) under reference numbers [GSE12368, GSE90713, GSE143383]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The overlap among the three datasets contained 206 genes as shown in the Venn diagram ( Figure 1D ), including 72 up-regulated and 134 down-regulated DEGs ( Table 1 ) between ACC tissues and normal tissues.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38053725", "locator": "sections[9] \"Identification of DEGs\" paragraph 2", "quote": "The overlap among the three datasets contained 206 genes as shown in the Venn diagram ( Figure 1D ), including 72 up-regulated and 134 down-regulated DEGs ( Table 1 ) between ACC tissues and normal tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The overlap among the three datasets contained 206 genes as shown in the Venn diagram ( Figure 1D ), including 72 up-regulated and 134 down-regulated DEGs ( Table 1 ) between ACC tissues and normal tissues.", "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:38053725"], "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:GSE12368"], "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:GSE12368"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38053725", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2023.1250033", "sha256": "sha256:2b5331145951d93b835f9e092b1447ab673c1e5ae9f497ce19b98974aa87714b", "bytes": 46296, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2023.1250033", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10694291", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12368", "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=GSE12368", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12368", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: The data that support the findings of this study are available in the GEO database (http://www.ncbi.nlm.nih.gov/geo) under reference numbers [GSE12368, GSE90713, GSE143383].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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