Identification of hub genes and potential molecular mechanisms in MSS/MSI classifier primary colorectal cancer based on multiple datasets.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39023715", "kind": "science-record", "revision": 3, "content_hash": "sha256:233444fbd6d9f7ef22e6d3599f2ba974d1706b1a66dd6620c2a20be9fea4e28a", "created_at": "2026-11-01T20:29:06Z", "updated_at": "2026-11-01T22:12:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and potential molecular mechanisms in MSS/MSI classifier primary colorectal cancer based on multiple datasets.", "doi": "10.1007/s12672-024-01148-0", "pmid": "39023715", "authors": ["Xia Qiao", "Duan Ma", "Xu Zhang"], "journal": "Discover oncology", "year": 2024, "abstract": "OBJECTIVE: MSI has a better prognosis than MSS in colorectal cancer patients, and the main objective of this study was to screen for differentially expressed molecules between MSI and MSS primary colorectal cancers using bioinformatics.\nMATERIAL AND METHODS: Two gene expression datasets (GSE13294 and GSE13067) were downloaded from GEO, and differential expressed genes (DEGs) were analyzed using GEO2R. Gene Ontology, Kyoto Encyclopedia of Genomes, and Gene Set Enrichment Analysis were conducted using the DEGs. Furthermore, a Protein-Protein Interaction Networks (PPI) was constructed to screen for significant modules and identify hub genes. The hub genes were analyzed in colorectal cancer using GEPIA. The expression of hub genes in clinical samples was visualized using the online Human Protein Atlas (HPA).\nRESULTS: A total of 265 common DEGs were identified in MSS primary colorectal cancer compared to MSI primary colorectal cancer. Among these, 178 DEGs were upregulated, and 87 DEGs were downregulated. Enrichment analysis showed that these DEGs were associated with the response to mechanical stimulus, regulation of cellular response to stress, G protein-coupled receptor binding, and other processes. A total of 5 hub genes was identified by cytoHubba: HNRNPL, RBM39, HNRNPH1, TRA2A, SRSF6. GEPIA software online analysis, 5 hub gene expression in colorectal cancer survival curve did not have significant differences. The expression of RBM39 was significantly different in different stages of colorectal cancer. The HPA online database results showed that the expression of the five hub proteins varied widely in CRC patients.\nCONCLUSION: The hub genes, such as HNRNPH1and RBM39, and the spliceosome resulting from DEGs, which may provide novel insights and evidence for the future diagnosis and targeted therapy of MSS/MSI PCRC.", "claims": [{"id": "claim-method", "statement": "DEGs (Differential Expressed Genes) were performed by GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/#). To obtain adjusted p-values (adj. P), we corrected the p-values using the Benjamini and Hochberg technique (false discovery rate) to achieved a trade-off between the possibility of false-positive results and the identification of statistically significant genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39023715", "locator": "sections[4] \"Screening of the DGEs\" paragraph 2", "quote": "DEGs (Differential Expressed Genes) were performed by GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/#)."}, {"asset": "source:pmid:39023715", "locator": "sections[4] \"Screening of the DGEs\" paragraph 2", "quote": "To obtain adjusted p-values (adj."}, {"asset": "source:pmid:39023715", "locator": "sections[4] \"Screening of the DGEs\" paragraph 2", "quote": "P), we corrected the p-values using the Benjamini and Hochberg technique (false discovery rate) to achieved a trade-off between the possibility of false-positive results and the identification of statistically significant genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is provided within the manuscript or supplementary information files. The bioinformation analysis datasets generated in the current study are available online as cited in the materials and methods.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39023715", "locator": "sections[24] \"notes\" paragraph 1", "quote": "Data is provided within the manuscript or supplementary information files. The bioinformation analysis datasets generated in the current study are available online as cited in the materials and methods."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 265 common DEGs were identified in MSS primary colorectal cancer compared to MSI primary colorectal cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39023715", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 265 common DEGs were identified in MSS primary colorectal cancer compared to MSI primary colorectal cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 265 common DEGs were identified in MSS primary colorectal cancer compared to MSI primary colorectal 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:39023715"], "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:GSE13067"], "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:GSE13067"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39023715", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-024-01148-0", "sha256": "sha256:d887f28f2c0f6cd2be844282fcb992e262d751dc1580dd5500c918957031305c", "bytes": 27856, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-024-01148-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11258107", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13067", "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=GSE13067", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13067", "version": null, "note": "Data is provided within the manuscript or supplementary information files. 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