Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32802507", "kind": "science-record", "revision": 8, "content_hash": "sha256:cb614918e14d8e34c941fbf58fdef3c7937a8479df4a303ac280fdab597fd105", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection.", "doi": "10.1155/2020/6285987", "pmid": "32802507", "authors": ["Ping Yang", "Junjie Liu", "Tianci Yang", "Lei Zhang", "Peiyou Gong", "Boqing Li", "Xiuzhi Zhou"], "journal": "Biochemistry research international", "year": 2020, "abstract": "BACKGROUND: Helicobacter pylori (H. pylori) is a common human pathogen, which is closely correlated with gastric cancer (GC). However, the mechanism of H. pylori-related GC has not been elucidated. This study aimed to explore the role of H. pylori infection in GC and find biomarkers for early diagnosis of H. pylori-related GC.\nMETHODS: We identified differentially expressed microRNAs (DEMs) and genes (DEGs) from the Gene Expression Omnibus (GEO) dataset, constructed microRNA-(miRNA-)mRNA expression networks, analyzed the function and signal pathway of cross-genes, analyzed the relations between cross-genes and GC prognosis with the Cancer Genome Atlas (TCGA) data, and verified the expression of cross-genes in patients with H. pylori infection.\nRESULTS: 22 DEMs and 68 DEGs were identified in GSE197694 and GSE27411 dataset. 16 miRNAs and 509 genes were involved in the expression network, while the cross-genes of the network were mainly enriched in MAP kinase (MAPK) signaling pathway and TGF-beta signaling pathway. Patients with higher expression of hsa-miR-196b-3p, CALML4, or SMAD6 or lower expression of PITX2 or TGFB2 had better outcomes than those with lower expression of hsa-miR-196b-3p, CALML4, or SMAD6 or higher expression of PITX2 or TGFB2 (P < 0.05). Patients with H. pylori infection had a higher expression of hsa-miR-196b-3p and CALML4 than those without H. pylori infection (P < 0.05).\nCONCLUSION: The study of miRNA-mRNA expression network would provide molecular support for early diagnosis and treatment of H. pylori-related GC.", "claims": [{"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32802507", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "state": "complete"}], "gaps": []}, "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:32802507"], "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:GSE19769"], "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": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate adjustment; source data"}, "inputs": ["data:geo:GSE19769"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32802507", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/6285987", "sha256": "sha256:576e5d829dbacb0034de4414ab1a98189214ec2ac9cc0ddb308389934154c4fa", "bytes": 36653, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/6285987", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7410007", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19769", "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=GSE19769", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19769", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM493633", "GSM493634", "GSM493635", "GSM493636", "GSM493637", "GSM493638", "GSM493639", "GSM493640", "GSM493641", "GSM493642", "GSM493643", "GSM493644", "GSM493645", "GSM493646", "GSM493647", "GSM493648", "GSM493649", "GSM493650", "GSM493651"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "9081", "taxon": "Homo sapiens", "title": "miRNA expression signatures for human stomach biopsy samples, H. pylori positive versus negative", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE27411", "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=GSE27411", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27411", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM677730", "GSM677731", "GSM677732", "GSM677733", "GSM677734", "GSM677735", "GSM677736", "GSM677737", "GSM677738", "GSM677739", "GSM677740", "GSM677741", "GSM677742", "GSM677743", "GSM677744", "GSM677745", "GSM677746", "GSM677747"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "6255", "taxon": "Homo sapiens", "title": "Transcriptional analysis reveals the molecular details of atrophic gastritis in Helicobacter pylori infected corpus mucosa", "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:32802507:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:15d591098eb1847c8ace3949d16533763d39d07b3bda933b7af97d66cf348587", "bytes": 463, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#tab1", "version": null, "note": "Summary of clinical information of 69 patients.", "structure": {"pmcid": "PMC7410007", "section_index": 8, "section_title": "2.6. Patient Data", "row_count": 13, "column_count": 2}, "table": {"label": "Table 1", "caption": "Summary of clinical information of 69 patients.", "rows": [["Characteristics", "Patients (n)"], ["Age (year)", ""], ["≤60", "31"], [">60", "38"], ["Sex", ""], ["Male", "46"], ["Female", "23"], ["Histopathological type", ""], ["Gastritis", "32"], ["Gastric adenocarcinoma", "37"], ["H. pylori infection", ""], ["Negative", "18"], ["Positive", "51"]], "row_count": 13, "column_count": 2, "numeric_cells": 10, "header_rows": 1, "locator": "section[8]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:32802507:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:151f09184be0dee792afdef54e13851aee5dd8edd8a8a6a46d001d297fdc6578", "bytes": 2123, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab2", "version": null, "note": "Differential expression of miRNAs of H. pylori-negative and -positive patients.", "structure": {"pmcid": "PMC7410007", "section_index": 13, "section_title": "3.1. Identification of DEMs and DEGs", "row_count": 23, "column_count": 7}, "table": {"label": "Table 2", "caption": "Differential expression of miRNAs of H. pylori-negative and -positive patients.", "rows": [["miRNA ID", "LogFC", "t", "B", "P value", "Adj. P value", "Expression"], ["hsa-miR-455", "−1.29961", "−13.2889", "14.50158", "1.32E − 10", "6.20E − 08", "Down"], ["hsa-miR-223", "2.015725", "7.995567", "7.036115", "2.91E − 07", "5.02E − 05", "Up"], ["hsa-miR-200a-5p", "−1.04839", "−7.29849", "5.792449", "1.02E − 06", "9.54E − 05", "Down"], ["hsa-miR-146b", "1.846493", "7.098055", "5.422075", "1.47E − 06", "0.000115", "Up"], ["hsa-miR-200a-3p", "−1.18346", "−6.46158", "4.208209", "4.97E − 06", "0.000249", "Down"], ["hsa-miR-155", "1.41517", "6.230643", "3.753807", "7.83E − 06", "0.000335", "Up"], ["hsa-miR-411", "−1.54782", "−5.84129", "2.971589", "1.71E − 05", "0.00062", "Down"], ["hsa-miR-551b", "−1.30788", "−5.44908", "2.164424", "3.85E − 05", "0.000994", "Down"], ["hsa-miR-142-3p", "1.67688", "5.430155", "2.12503", "4.00E − 05", "0.000994", "Up"], ["hsa-miR-203", "−1.63669", "−5.12951", "1.494025", "7.54E − 05", "0.001476", "Down"], ["hsa-miR-142-5p", "1.677953", "5.051426", "1.32866", "8.90E − 05", "0.001609", "Up"], ["hsa-miR-153", "−1.47449", "−4.88801", "0.980864", "0.000126", "0.002045", "Down"], ["hsa-miR-204", "−1.55239", "−4.24223", "−0.41065", "0.000513", "0.006184", "Down"], ["hsa-miR-196b", "1.594266", "3.80117", "−1.36658", "0.001355", "0.012736", "Up"], ["hsa-miR-509", "1.069763", "3.765869", "−1.44288", "0.001465", "0.013238", "Up"], ["hsa-miR-326", "−1.20269", "−3.53852", "−1.93239", "0.002417", "0.019915", "Down"], ["hsa-miR-146a", "1.324456", "3.446357", "−2.1296", "0.00296", "0.022082", "Up"], ["hsa-miR-299-5p", "−1.04861", "−3.32334", "−2.39132", "0.003877", "0.027607", "Down"], ["hsa-miR-520e", "1.32247", "3.302749", "−2.43493", "0.004055", "0.028448", "Up"], ["hsa-miR-650", "1.709805", "3.294791", "−2.45177", "0.004127", "0.028522", "Up"], ["hsa-miR-138", "1.114925", "3.195115", "−2.6619", "0.00513", "0.033381", "Up"], ["hsa-miR-368", "−1.02603", "−3.19023", "−2.67214", "0.005185", "0.033381", "Down"]], "row_count": 23, "column_count": 7, "numeric_cells": 132, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:32802507:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c848761bdfa67ec835b58a78474ebe0fa93e112d08cf1b81710aa8ea316c064a", "bytes": 2404, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tab3", "version": null, "note": "Top 10 GO functions of the cross-genes in the network.", "structure": {"pmcid": "PMC7410007", "section_index": 15, "section_title": "3.3. GO and KEGG Analysis of Cross-Genes in the Network", "row_count": 33, "column_count": 4}, "table": {"label": "Table 3", "caption": "Top 10 GO functions of the cross-genes in the network.", "rows": [["Category", "Gene terms", "Count", "P value"], ["Biological process", "GO:0003148, outflow tract septum morphogenesis", "10", "1.24E − 09"], ["GO:0003151, outflow tract morphogenesis", "15", "3.98E − 09"], ["GO:0001655, urogenital system development", "30", "6.76E − 09"], ["GO:0003279, cardiac septum development", "17", "1.22E − 08"], ["GO:0060411, cardiac septum morphogenesis", "13", "1.60E − 07"], ["GO:0010632, regulation of epithelial cell migration", "26", "1.74E − 07"], ["GO:0010631, epithelial cell migration", "29", "1.75E − 07"], ["GO:0061564, axon development", "33", "1.77E − 07"], ["GO:0043542, endothelial cell migration", "25", "1.77E − 07"], ["GO:0090132, epithelium migration", "29", "2.09E − 07"], [""], ["Cellular component", "GO:0005667, transcription factor complex", "23", "4.28E − 07"], ["GO:0097060, synaptic membrane", "26", "9.71E − 06"], ["GO:0045211, postsynaptic membrane", "21", "2.70E − 05"], ["GO:0099699, integral component of synaptic membrane", "14", "3.31E − 05"], ["GO:0005912, adherens junction", "28", "7.12E − 05"], ["GO:0099240, intrinsic component of synaptic membrane", "14", "7.62E − 05"], ["GO:0033267, axon part", "22", "0.000108619"], ["GO:0000790, nuclear chromatin", "20", "0.000128584"], ["GO:0099055, integral component of postsynaptic membrane", "11", "0.000162968"], ["GO:0000151, ubiquitin ligase complex", "16", "0.000198327"], [""], ["Molecular function", "GO:0000978, RNA polymerase II proximal promoter sequence-specific DNA binding", "38", "5.75E − 10"], ["GO:0000987, proximal promoter sequence-specific DNA binding", "39", "5.92E − 10"], ["GO:0035326, enhancer binding", "19", "1.24E − 09"], ["GO:0000980, RNA polymerase II distal enhancer sequence-specific DNA binding", "15", "1.89E − 08"], ["GO:0001158 enhancer sequence-specific DNA binding", "16", "5.18E − 08"], ["GO:0003682, chromatin binding", "34", "9.92E − 08"], ["GO:0001228, DNA-binding transcription activator activity, RNA polymerase II-specific", "29", "2.20E − 06"], ["GO:0004714, transmembrane receptor protein tyrosine kinase activity", "9", "7.94E − 06"], ["GO:0003712, transcription coregulator activity", "32", "1.19E − 05"], ["GO:0019199, transmembrane receptor protein kinase activity", "10", "1.30E − 05"]], "row_count": 33, "column_count": 4, "numeric_cells": 90, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:32802507:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:569f5007a3362aa53a4316ad2ea4c753057faff632ded54be53d997f9bc0c413", "bytes": 797, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#tab4", "version": null, "note": "Top 10 KEGG pathways of the cross-genes in the network.", "structure": {"pmcid": "PMC7410007", "section_index": 15, "section_title": "3.3. 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The Benjamini and Hochberg false discovery rate (FDR) method was used to adjust the P value to reduce the false-positive risk.” “The miRNA expression profile (GSE19769) [7] and the gene expression profile (GSE27411) [17] were included in this study.”"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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