A Bioinformatic Profile of Gene Expression of Colorectal Carcinoma Derived Organoids.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30363662", "kind": "science-record", "revision": 3, "content_hash": "sha256:428247798568626534eb6027fc088ebda8bae92ae3677ed4a58c8242a7f80295", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T21:21:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Bioinformatic Profile of Gene Expression of Colorectal Carcinoma Derived Organoids.", "doi": "10.1155/2018/2594076", "pmid": "30363662", "authors": ["Peng A", "Xinyi Xu", "Chenglin Wang", "Ling Ye", "Jing Yang"], "journal": "BioMed research international", "year": 2018, "abstract": "Colorectal carcinoma is one of the common cancers in human. It has been intensely debated whether the in vitro cancer cell lines are closely enough for recapitulating the original tumor in understanding the molecular characteristic of CRC. Organoid as a new in vitro 3D culture system has sprang out in CRC study for the capability in reviving the original tissue. The aim of this study is to profile the gene expression of CRC organoid. The gene expression GSE64392 was from GEO database contained 20-patients-derived 37 organoid samples, including 22 colorectal tumor organoid samples and 15 paired healthy samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied for classifying differentially expressed genes (DEGs). Protein interaction among DEGs was analyzed by Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. In total, 853 gene sequences were identified. GO analysis revealed that DEGs were extensively involved in various biological process (BP), like proliferation, cell cycle, and biosynthesis. KEEG pathway analysis showed that WNT, MAPK, TGF-β, SHH, ECM-receptor interaction, and FGF pathways were altered. DEGs which were identified with protein interactions were major response for extracellular matrix organization and the GPCR pathway. In conclusion, our study profiled the DEGs in CRC organoids and promotes our understanding of the CRC organoids as a new model for colorectal cancer research.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes were analyzed with the GEO2R, which accompanies with the GEO dataset and is supported by GEO database and available at https://www.ncbi.nlm.nih.gov/geo. Data were analyzed with default parameters. Genes with Log2-fold change between tumor and healthy samples ≥1 or ≤-1 were classified as differentially expressed genes (DEGs) and the adjusted P-value (adj.P.Val) < 0.05 was considered as statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30363662", "locator": "sections[4] \"2.2. 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Genes with Log2-fold change between tumor and healthy samples ≥1 or ≤-1 were classified as differentially expressed genes (DEGs) and the adjusted P-value (adj.P.Val) < 0.05 was considered as statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30363662", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30363662"], "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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