Identification of the Hub Genes and Potential Regulation Network in Chronic Hepatitis B via Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36193503", "kind": "science-record", "revision": 4, "content_hash": "sha256:30e035260b6ed88289d7a1303dafff940ce7bf8b6bd1f5455f9d2ce04e66955b", "created_at": "2026-11-01T18:15:30Z", "updated_at": "2026-11-01T22:07:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the Hub Genes and Potential Regulation Network in Chronic Hepatitis B via Bioinformatics Analysis.", "doi": "10.1155/2022/6113807", "pmid": "36193503", "authors": ["Jingjing Fan", "Yong Chen", "Wei Zhang", "Xiaoying Zhou", "Xue Bai", "Caifang Chang", "Yongping Han", "Jinlu Liu"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Chronic hepatitis B (CHB) is a serious infectious disease which is induced by hepatitis B virus (HBV) infection. This project was conducted to reveal the potential mechanism in CHB development via analyzing the public clinical data.\nMethods: GSE33857 and GSE110217, obtained from the GEO database, were used for bioinformatics excavation. Briefly, the raw data of GSE33857 and GSE110217 were analyzed with the GEO2R, and then the expressed matrix files were generated. The matrix files was visualized as heat map with R software. The targets of the miRNAs were analyzed with the miRDIP database. The functional annotation and pathway enrichment were performed using \"clusterProfiler\" package in R software. The STRING database was utilized to analyze the interaction of the DEGs, and the PPI and miRNA-mRNA network were established according to the related results.\nResults: 93 downregulated genes and 17 upregulated genes in GES33857, and 111 downregulated and 40 upregulated genes in GSE110217 were identified as the hub nodes. The targets of the DEGs in the datasets were enriched in PI3K/AKT and MAPK pathways and associated with transcriptional regulation. Moreover, PPI and miRNA-mRNA networks were also established with the DEGs and related targets in the datasets. miR-122-5p, miR-125b-5p, miR-136-5p, miR-194-5p, miR-139-5p, miR-140-5p, miR-181a-5p, and miR-29b-3p were identified as the potential biomarkers in CHB.\nConclusion: Eight miRNAs, including miR-122-5p, miR-125b-5p, miR-136-5p, miR-194-5p, miR-139-5p, miR-140-5p, miR-181a-5p, and miR-29b-3p, were identified as the potential biomarkers in CHB, and the PPI and miRNA-mRNA networks were also established.", "claims": [{"id": "claim-method", "statement": "The GSE33857 and GSE110217 were analyzed with the GEO2R to identify the DEGs in the progression of CHB.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36193503", "locator": "sections[8] \"3.1. Identification of the DEGs\" paragraph 2", "quote": "The GSE33857 and GSE110217 were analyzed with the GEO2R to identify the DEGs in the progression of CHB."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data to support the findings of this study is available on reasonable request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36193503", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "Data to support the findings of this study is available on reasonable request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "93 downregulated genes and 17 upregulated genes were found in the GES33857, and 111 downregulated and 40 upregulated genes were found in the GSE110217.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36193503", "locator": "sections[8] \"3.1. Identification of the DEGs\" paragraph 2", "quote": "In the results, 93 downregulated genes and 17 upregulated genes were found in the GES33857, and 111 downregulated and 40 upregulated genes were found in the GSE110217 (Figures 1(a) and 1(b))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "93 downregulated genes and 17 upregulated genes were found in the GES33857, and 111 downregulated and 40 upregulated genes were found in the GSE110217.", "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:36193503"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36193503", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/6113807", "sha256": "sha256:b7f605f893fdb5fbb6a6a31b9dad91a8744b7772486fb75ab993da552772691b", "bytes": 23138, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/6113807", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9525735", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The GSE33857 and GSE110217 were analyzed with the GEO2R to identify the DEGs in the progression of CHB."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["GSE33857 (GPL10656)", "GSE110217 (GPL15018)"], "resolved_accessions": [], "statements": ["Data to support the findings of this study is available on reasonable request from the corresponding author."], "basis": "The paper names GSE33857 (GPL10656), GSE110217 (GPL15018), but the accession does not resolve in the repository (no reason recorded, no reason recorded), so the data cannot be reached from here. 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