Identification of biomarkers for the diagnosis and treatment of primary colorectal cancer based on microarray technology.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35117711", "kind": "science-record", "revision": 5, "content_hash": "sha256:1784fed48b84f6153ea394b90345bb4909fa20157c0cc72873abe61785d1abb5", "created_at": "2026-11-01T17:36:51Z", "updated_at": "2026-11-01T22:48:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of biomarkers for the diagnosis and treatment of primary colorectal cancer based on microarray technology.", "doi": "10.21037/tcr-19-2290", "pmid": "35117711", "authors": ["Zhi Gang Zheng", "Bao Qing Ma", "Yu Xiao", "Tian Xi Wang", "Tian Yu", "Yu Hu Huo", "Qing Qing Wang", "Meng Jie Shan", "Ling Bing Meng", "Jing Han"], "journal": "Translational cancer research", "year": 2020, "abstract": "BACKGROUND: Primary colorectal cancer (PCRC) is one of the most common malignant tumors in clinic, and is characterized by high heterogeneity occurring between tumors and intracellularly. Therefore, this study aimed to explore potential gene targets for the diagnosis and treatment of PCRC via bioinformatic technology.\nMETHODS: Gene Expression Omnibus (GEO) was used to download the data used in this study. Differently expressed genes (DEGs) were identified with GEO2R, and the gene set enrichment analysis (GSEA) was implemented for enrichment analysis. Then, the researchers constructed a protein-protein interaction (PPI) network, a significant module, and a hub genes network.\nRESULTS: The GSE81558 dataset was downloaded, and a total of 97 DEGs were found. There were 23 up-regulated DEGs and 74 down-regulated DEGs in the PCRC samples, compared with the control group. The PPI network included a total of 42 nodes and 63 edges. One module network consisted of 11 nodes and 25 edges. Another module network consisted of 4 nodes and 6 edges. The hub genes network was created by cytoHubba using GCG, GUCA2B, CLCA4, ZG16, TMIGD1, GUCA2A, CHGA, PYY, SST, and MS4A12.\nCONCLUSIONS: Ten hub genes were found from the genomic samples of patients with PCRC and normal controls by bioinformatics analysis. The hub genes might provide novel ideas and evidence for the diagnosis and targeted therapy of PCRC.", "claims": [{"id": "claim-method", "statement": "To be exact, GEO2R is based on two R packages, GEOquery, and limma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117711", "locator": "sections[4] \"DEGs\" paragraph 2", "quote": "To be exact, GEO2R is based on two R packages, GEOquery, and limma."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE81558 [GPL15207 (PrimeView) Affymetrix Human Gene Expression Array] was downloaded from the GEO database. A total of 32 samples, which consisted of 9 control colorectum samples and 23 PCRC samples, were selected from the GSE81558 database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117711", "locator": "sections[3] \"Download data\" paragraph 2", "quote": "GSE81558 [GPL15207 (PrimeView) Affymetrix Human Gene Expression Array] was downloaded from the GEO database. A total of 32 samples, which consisted of 9 control colorectum samples and 23 PCRC samples, were selected from the GSE81558 database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Ten hub genes were identified as candidate genes associated with primary colorectal cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35117711", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Ten hub genes were found from the genomic samples of patients with PCRC and normal controls by bioinformatics analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Ten hub genes were identified as candidate genes associated with 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:35117711"], "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:GSE81558"], "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:GSE81558"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35117711", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-19-2290", "sha256": "sha256:7bbaf1208793690f7f90f83fd0b18d229129e59d024b652531048f4e78570803", "bytes": 25270, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-19-2290", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8798183", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE81558", "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=GSE81558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE81558", "version": null, "note": "GSE81558 [GPL15207 (PrimeView) Affymetrix Human Gene Expression Array] was downloaded from the GEO database. A total of 32 samples, which consisted of 9 control colorectum samples and 23 PCRC samples, were selected from the GSE81558 database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE81558 [GPL15207 (PrimeView) Affymetrix Human Gene Expression Array] was downloaded from the GEO database. 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