Predication of hub target genes of differentially expressed microRNAs contributing to Helicobacter pylori infection in gastric non-cancerous tissue.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32099601", "kind": "science-record", "revision": 9, "content_hash": "sha256:c835cc20b9d660b404f5f7d33a84da8a793bf8232f57aeabdd1c8543ebbb98f8", "created_at": "2026-11-01T15:40:57Z", "updated_at": "2026-11-01T22:44:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "Predication of hub target genes of differentially expressed microRNAs contributing to Helicobacter pylori infection in gastric non-cancerous tissue.", "doi": null, "pmid": "32099601", "authors": ["Mohsen Norouzinia", "Mona Zamanian Azodi", "Diba Najafgholizadeh Seyfi", "Ali Kardan", "Ali Naseh", "Zahra Akbari"], "journal": "Gastroenterology and hepatology from bed to bench", "year": 2019, "abstract": "AIM: The main goal of this investigation was to provide an overview on H.pylori effect on gastric tissue via bioinformatics analysis of microarray-identified miRNAs and its target genes.\nBACKGROUND: MicroRNAs which control about 30 to 60% of gene expression in human body play a critical role in different cell growth stages. Expression modification of non-coding (NC) RNAs in H.pylori infections requires further investigations to provide better understanding of their roles in the body.\nMETHODS: GSE54397, the microRNA microarray dataset, was analyzed by GEO2R, the online GEO database for detection of differentially expressed microRNAs and lastly the potential target genes as well as their associated pathways.\nRESULTS: A total of 244 miRNAs were detected as differentially expressed (p<0.05 and FC>2) in non-cancerous tissue of gastric with H.pylori infection in comparison with tissues without H.pylori infection. The findings indicated that hub microRNAs and target genes of up-regulated network are KIF9, DCTN3, and CA5BP1 along with hsa-miR-519d, hsa-miR-573, hsa-miR-646, hsa-miR-92a-1, hsa-miR-186, and hsa-miR-892a, respectively. For the down-regulated network, genes of RABGAP1, HSPB11 and microRNAs of hsa-miR-620, hsa-miR-19b-2, hsa-miR-555, and hsa-let-7f-2 were hubs. Most of the up-regulated microRNAs are involved in gastric cancer development while there is no evidence for the down-regulated ones. Yet, all of the hub down-regulated miRNAs are reported to have associations with different kinds of cancer.\nCONCLUSION: The introduced hub miRNAs and genes may serve as feasible markers in the mechanisms of H.pylori infection for different kinds of gastric diseases, in particular gastric cancer. However, their role requires further investigations.", "claims": [{"id": "claim-method", "statement": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), R-based which is a GEO online tool analyzed the differentially expressed microRNAs of the mentioned dataset. Specifically, two groups of samples from four groups were selected for this investigation. The first two groups were cancerous tissue HP+ and HP- while the other two groups were noncancerous regions HP+ and HP-, 32 samples altogether. This online tool analyzes DE-miRNAs by performing statistical analysis of t-test or analysis of variance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32099601", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), R-based which is a GEO online tool analyzed the differentially expressed microRNAs of the mentioned dataset. Specifically, two groups of samples from four groups were selected for this investigation. The first two groups were cancerous tissue HP+ and HP- while the other two groups were noncancerous regions HP+ and HP-, 32 samples altogether. This online tool analyzes DE-miRNAs by performing statistical analysis of t-test or analysis of variance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset chosen for our study was the GEO Accession number of GSE54397 under the platform of GPL15159 (Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840) available on Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32099601", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "The dataset chosen for our study was the GEO Accession number of GSE54397 under the platform of GPL15159 (Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840) available on Gene Expression Omnibus (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:32099601"], "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:GSE54397"], "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:GSE54397"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32099601", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:5d8a37f377d0fb0290e361d4280cf2da181b22ae4e9e709fdfc7dde27daeab5c", "bytes": 20396, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "32099601", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7011053", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE54397", "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=GSE54397", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54397", "version": null, "note": "The dataset chosen for our study was the GEO Accession number of GSE54397 under the platform of GPL15159 (Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840) available on Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset chosen for our study was the GEO Accession number of GSE54397 under the platform of GPL15159 (Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840) available on Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1314316", "GSM1314317", "GSM1314318", "GSM1314319", "GSM1314320", "GSM1314321", "GSM1314322", "GSM1314323", "GSM1314324", "GSM1314325", "GSM1314326", "GSM1314327", "GSM1314328", "GSM1314329", "GSM1314330", "GSM1314331", "GSM1314332", "GSM1314333", "GSM1314334", "GSM1314335", "GSM1314336", "GSM1314337", "GSM1314338", "GSM1314339", "GSM1314340", "GSM1314341", "GSM1314342", "GSM1314343", "GSM1314344", "GSM1314345", "GSM1314346", "GSM1314347"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "15159", "taxon": "Homo sapiens", "title": "microRNA expressions in gastric cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32099601:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6c3faaa01f7f794324f68c4b62d73df1c1ca7955fb28bdd253a6853bd7d7d1a8", "bytes": 782, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "The list of target genes of up-regulated miRNAs detected by miRanda source, CluePedia. 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Kappa Score:0.6 was considered for analysis", "structure": {"pmcid": "PMC7011053", "section_index": 3, "section_title": "Results", "row_count": 11, "column_count": 5}, "table": {"label": "Table 2", "caption": "The list of target genes of down-regulated miRNAs detected by miRanda source, CluePedia. 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BACK", "ospital and the end the samples was used for microarray study. The 250 identified DE-miRNAs were ran", "in the body. METHODS: GSE54397, the microRNA microarray dataset, was analyzed by GEO2R, the online G"], "order_basis": "paper_text_order:240", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), R-based which is a GEO online tool analyzed the differentially expressed microRNAs of the mentioned dataset. Specifically, two groups of samples from four groups were selected for this investigation. The first two groups were cancerous tissue HP+ and HP- while the other two groups were noncancerous regions HP+ and HP-, 32 samples altogether. This online tool analyzes DE-miRNAs by performing statistical analysis of t-test or analysis of variance."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}