Identification of Hub Genes in Colorectal Adenocarcinoma by Integrated Bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35693937", "kind": "science-record", "revision": 4, "content_hash": "sha256:507d2d6e61fdd0195a03eb154d61d3e1efd9ad09157483784ffec868218d3b58", "created_at": "2026-11-01T18:14:40Z", "updated_at": "2026-11-01T22:06:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes in Colorectal Adenocarcinoma by Integrated Bioinformatics.", "doi": "10.3389/fcell.2022.897568", "pmid": "35693937", "authors": ["Yang Liu", "Lanlan Chen", "Xiangbo Meng", "Shujun Ye", "Lianjun Ma"], "journal": "Frontiers in cell and developmental biology", "year": 2022, "abstract": "An improved understanding of the molecular mechanism of colorectal adenocarcinoma is necessary to predict the prognosis and develop new target gene therapy strategies. This study aims to identify hub genes associated with colorectal adenocarcinoma and further analyze their prognostic significance. In this study, The Cancer Genome Atlas (TCGA) COAD-READ database and the gene expression profiles of GSE25070 from the Gene Expression Omnibus were collected to explore the differentially expressed genes between colorectal adenocarcinoma and normal tissues. The weighted gene co-expression network analysis (WGCNA) and differential expression analysis identified 82 differentially co-expressed genes in the collected datasets. Enrichment analysis was applied to explore the regulated signaling pathway in colorectal adenocarcinoma. In addition, 10 hub genes were identified in the protein-protein interaction (PPI) network by using the cytoHubba plug-in of Cytoscape, where five genes were further proven to be significantly related to the survival rate. Compared with normal tissues, the expressions of the five genes were both downregulated in the GSE110224 dataset. Subsequently, the expression of the five hub genes was confirmed by the Human Protein Atlas database. Finally, we used Cox regression analysis to identify genes associated with prognosis, and a 3-gene signature (CLCA1-CLCA4-GUCA2A) was constructed to predict the prognosis of patients with colorectal cancer. In conclusion, our study revealed that the five hub genes and CLCA1-CLCA4-GUCA2A signature are highly correlated with the development of colorectal adenocarcinoma and can serve as promising prognosis factors to predict the overall survival rate of patients.", "claims": [{"id": "claim-method", "statement": "In this study, WGCNA and differential gene expression analysis was performed to analyze the mRNA expression data of COAD-READ in TCGA and GEO databases, and the differentially co-expressed genes were obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35693937", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "In this study, WGCNA and differential gene expression analysis was performed to analyze the mRNA expression data of COAD-READ in TCGA and GEO databases, and the differentially co-expressed genes were obtained."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. 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These data can be found at: the TCGA database (https://portal.gdc.cancer.gov/) and GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integrating weighted gene co-expression network analysis and differential gene expression analysis identified five survival-related hub genes and a three-gene prognostic signature for colorectal adenocarcinoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35693937", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In conclusion, our study revealed that the five hub genes and CLCA1–CLCA4–GUCA2A signature are highly correlated with the development of colorectal adenocarcinoma and can serve as promising prognosis factors to predict the overall survival rate of patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integrating weighted gene co-expression network analysis and differential gene expression analysis identified five survival-related hub genes and a three-gene prognostic signature for colorectal adenocarcinoma.", "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:35693937"], "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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