SRC and TP53 play critical role in low-grade dysplasia colorectal mucosa transformation into cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30774815", "kind": "science-record", "revision": 8, "content_hash": "sha256:29b94b765bb755ed6f3a5664c134ba45b78c20da75104a9a920286d3569c1e0a", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:00:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "SRC and TP53 play critical role in low-grade dysplasia colorectal mucosa transformation into cancer.", "doi": null, "pmid": "30774815", "authors": ["Hamid Asadzadeh-Aghdaei", "Mona Zamanian Azodi", "Reza Vafaee", "Hamideh Moravvej Farshi", "Nosratollah Naderi"], "journal": "Gastroenterology and hepatology from bed to bench", "year": 2018, "abstract": "AIM: Determination of crucial genes that are involved in onset and progress of dysplasia of colorectal mucosa is the aim of this study.\nBACKGROUND: Management of dysplasia as one of the risk factors of colon cancer is very challenging. Molecular studies could be helpful in this matter. Here, the transcriptome profile of low-grade dysplasia in colon tissue in comparison with normal one is studied by protein-protein interaction (PPI) network analysis.\nMETHODS: For detecting differentially expressed genes (DEGs) of dysplasia lesion, the data was downloaded from the gene chip GSE31106, platform GPL1261, GSM770092-94 as normal colorectal mucosa group and GSM770098-100 as low-grade dysplasia colorectal mucosa from the Gene Expression Omnibus database (GEO). The expression profile is evaluated by GEO2R and a network of DEGs is constructed and analyzed by Cytoscape algorithms.\nRESULTS: The findings indicate that a PPI network analysis of 113 DEGs is consist of 8 nodes that 6 of them are common with inflammation state. Only SRC and TP53 were recognized as the specific makers for dysplasia. In this respect, a subnetwork of these two genes introduce a panel of 8 nodes consist of HRAS, MYC, PIK3CA, PIK3CB, PIK3CD, PIK3CG, SRC, and TP53.\nCONCLUSION: It can be concluded that SRC and TP53 may play prominent role in dysplasia pathogenicity after running validation tests.", "claims": [{"id": "claim-method", "statement": "Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774815", "locator": "sections[2] \"Methods\" paragraph 7", "quote": "Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Series GSE31106, platform GPL1261, GSM770092-94 as normal colorectal mucosa group and GSM770098-100 as low-grade dysplasia colorectal mucosa group were downloaded from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774815", "locator": "sections[2] \"Methods\" paragraph 3", "quote": "Series GSE31106, platform GPL1261, GSM770092-94 as normal colorectal mucosa group and GSM770098-100 as low-grade dysplasia colorectal mucosa group were downloaded from GEO database."}], "state": "complete"}], "gaps": ["doi"]}, "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:30774815"], "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:GSE31106"], "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:GSE31106"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30774815", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:78e799df9eaa686c4f5739b563105382e17f65693291fe7840634be8aeec97fc", "bytes": 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"GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Series GSE31106, platform GPL1261, GSM770092-94 as normal colorectal mucosa group and GSM770098-100 as low-grade dysplasia colorectal mucosa group were downloaded from GEO database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM770092", "GSM770093", "GSM770094", "GSM770095", "GSM770096", "GSM770097", "GSM770098", "GSM770099", "GSM770100", "GSM770101", "GSM770102", "GSM770103", "GSM770104", "GSM770105", "GSM770106", "GSM770107", "GSM770108", "GSM770109"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Expression data for the different phases of ulcerative colitis-associated carcinogenesis in a mouse model", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": 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