The Effect of Salmonella AvrA Infection on Colon Cancer: An in-silico Study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36708565", "kind": "science-record", "revision": 3, "content_hash": "sha256:bc4aace45e6423e05948a2afc0a0dc7f92bbef7192bb47daac8c8d54d7db8047", "created_at": "2026-11-01T19:01:16Z", "updated_at": "2026-11-01T22:08:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Effect of Salmonella AvrA Infection on Colon Cancer: An in-silico Study.", "doi": "10.31557/APJCP.2023.24.1.163", "pmid": "36708565", "authors": ["Bogi Pratomo Wibowo", "Handono Kalim", "Husnul Khotimah", "Hidayat Sujuti", "Reza Ardi Wibowo"], "journal": "Asian Pacific journal of cancer prevention : APJCP", "year": 2023, "abstract": "OBJECTIVE: Colorectal cancer (CRC) is one of the main causes of morbidity and mortality due to cancer. The purpose of this in-silico study was to examine the relationship of chronic infection mechanisms caused by Salmonella Anti virulence agent A (AvrA) to gene mutations in the carcinogenic process of CRC.\nMETHODS: Gene expression data on the mouse colon was obtained from the GSE22215 dataset | Gene Expression Omnibus (GEO). Adjusted p-value was calculated using Benjamini & Hochberg False Discovery Rate (FDR<0.01). Gene expression in colon adenocarcicoma tumors was obtained from The Cancer Genome Atlas's (TCGA) Genomic Data Commons (GDC) dataset containing 458 colon tumor samples.\nRESULT: Expressions of MLH1, MSH2, EPCAM, APC, and PMS2 in cases of colon adenocarcinoma tumor showed a correlation with genes that underwent changes due to Salmonella AvrA infection. Among the gens of interest, EPCAM was the gene that had the highest correlation compared to other genes (MLH1, MSH2, APC, and PMS2) (n= 514, Gene r-p value < 0.01 =22355). There were 514 genes that had a correlation with cases of AvrA infection. Tumor Necrosis Factor (TNF), which is a gene that is upregulated in AvrA infection and correlates negatively with EPCAM, had the highest BC value compared to other gens (p= 0.0000768). Survival probability showed that EPCAM was highly expressed and it can increase survival time. In addition to TNF, our study indicated that IL1B (p= 0.000419), S100A8 (p= 2.02E-05), S100A9 (p=0.000419) correlated with the gene of interest.\nCONCLUSION: Late Salmonella AvrA infection affects the expression of genes involved in inflammation in colorectal cancer samples.", "claims": [{"id": "claim-method", "statement": "The adjustment p-value was calculated using Benjamini & Hochberg (False discovery rate) (FDR <0.01).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36708565", "locator": "sections[2] \"Materials and Methods\" paragraph 3", "quote": "The adjustment p-value was calculated using Benjamini & Hochberg (False discovery rate) (FDR <0.01)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression data on the mouse colon was obtained from the GSE22215 dataset | Gene Expression Omnibus (GEO). The dataset contained gene expressions undergone changes in the late phase (4 days of treatment) with Salmonella strain SL1344 (AvrA expression) infection and HBSS sterile treatment (control).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36708565", "locator": "sections[2] \"Materials and Methods\" paragraph 3", "quote": "Gene expression data on the mouse colon was obtained from the GSE22215 dataset | Gene Expression Omnibus (GEO). The dataset contained gene expressions undergone changes in the late phase (4 days of treatment) with Salmonella strain SL1344 (AvrA expression) infection and HBSS sterile treatment (control)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Late Salmonella AvrA infection affects the expression of genes involved in inflammation in colorectal cancer samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36708565", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Late Salmonella AvrA infection affects the expression of genes involved in inflammation in colorectal cancer samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Late Salmonella AvrA infection affects the expression of genes involved in inflammation in colorectal cancer samples.", "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:36708565"], "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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METHODS: Gene expression data on the mouse colon was obtained from the GSE22215 dataset", "ple Collection 1 Gene expression data on the mouse colon was obtained from the GSE22215 dataset", "t was microarrays [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version"], "order_basis": "paper_text_order:377", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Centrality"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}