Transcriptome Classification Reveals Molecular Subgroups in Patients with Hepatitis B Virus.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33859718", "kind": "science-record", "revision": 7, "content_hash": "sha256:f9a3d9cf30a2f507ba8dce5344cd28de36a825e5b4726c3ad9495f25c6f77803", "created_at": "2026-11-01T15:41:32Z", "updated_at": "2026-11-01T22:03:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome Classification Reveals Molecular Subgroups in Patients with Hepatitis B Virus.", "doi": "10.1155/2021/5543747", "pmid": "33859718", "authors": ["Conghui Zhang", "Jie Li", "Lan Yang", "Fengxia Xu", "Huiyuan She", "Xinghui Liu"], "journal": "Computational and mathematical methods in medicine", "year": 2021, "abstract": "Hepatitis B virus (HBV) specifically infects hepatocytes, which can cause progressive liver fibrosis and a significantly increased risk of liver cancer. Multiple studies indicated host genetic, virological, and immunological factors could affect the HBV infection. However, the underlying mechanism involved in HBV infection remained unclear. Based on the analysis of gene expression data of 124 HBV patients (GEO accession: GSE84044), molecular subgroups of patients infected with hepatitis B virus were identified in this study, including C1, C2, and C3 groups. The age, fiber, degree of chemical and inflammation, and gene expression difference were also compared among the three sampling groups. Furthermore, the liver index was calculated using 93 liver-specific genes. The liver-specific gene expression in different molecular subgroups of HBV patients was thoroughly analyzed and then was compared with fibrosis and inflammation levels. Results showed that the C2 group was the youngest and the C3 group had the highest degree of fibrosis and inflammation. Enrichment analysis showed that metabolism-related pathways were mainly expressed in the C1 and C2 groups, and inflammation-related pathways and proteoglycans in cancer were highly expressed in the C1 and C3 groups. The liver index was higher in the C2 group than in the C1 and C3 groups, and it was the lowest in the C3 group. Macrophage M1/M2 and neutrophils were significantly different in the three groups. M1 was mainly abundant in the C3 group, and M2 and neutrophils were mainly abundant in the C2 group. This study provides novel information to understand the mechanisms of HBV infection in chronic hepatitis B (CHB) patients.", "claims": [{"id": "claim-data-access", "statement": "Previously reported gene expression and clinical data were used to support this study and are available at Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/gds). These prior studies (and datasets) are cited at relevant places within the text as references.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33859718", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "Previously reported gene expression and clinical data were used to support this study and are available at Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/gds). These prior studies (and datasets) are cited at relevant places within the text as references."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33859718"], "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:GSE84044"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE84044"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33859718", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/5543747", "sha256": "sha256:fdfff30eb77873e3916dfff64ea6aae9596f4b0307f6adbf691a665f871fa47f", "bytes": 29756, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/5543747", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8028738", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84044", "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=GSE84044", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84044", "version": null, "note": "Previously reported gene expression and clinical data were used to support this study and are available at Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/gds). These prior studies (and datasets) are cited at relevant places within the text as references.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Previously reported gene expression and clinical data were used to support this study and are available at Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/gds). These prior studies (and datasets) are cited at relevant places within the text as references.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2226280", "GSM2226281", "GSM2226282", "GSM2226283", "GSM2226284", "GSM2226285", "GSM2226286", "GSM2226287", "GSM2226288", "GSM2226289", "GSM2226290", "GSM2226291", "GSM2226292", "GSM2226293", "GSM2226294", "GSM2226295", "GSM2226296", "GSM2226297", "GSM2226298", "GSM2226299", "GSM2226300", "GSM2226301", "GSM2226302", "GSM2226303", "GSM2226304", "GSM2226305", "GSM2226306", "GSM2226307", "GSM2226308", "GSM2226309", "GSM2226310", "GSM2226311", "GSM2226312", "GSM2226313", "GSM2226314", "GSM2226315", "GSM2226316", "GSM2226317", "GSM2226318", "GSM2226319", "GSM2226320", "GSM2226321", "GSM2226322", "GSM2226323", "GSM2226324", "GSM2226325", "GSM2226326", "GSM2226327", "GSM2226328", "GSM2226329", "GSM2226330", "GSM2226331", "GSM2226332", "GSM2226333", "GSM2226334", "GSM2226335", "GSM2226336", "GSM2226337", "GSM2226338", "GSM2226339", "GSM2226340", "GSM2226341", "GSM2226342", "GSM2226343", "GSM2226344", "GSM2226345", "GSM2226346", "GSM2226347", "GSM2226348", "GSM2226349", "GSM2226350", "GSM2226351", "GSM2226352", "GSM2226353", "GSM2226354", "GSM2226355", "GSM2226356", "GSM2226357", "GSM2226358", "GSM2226359", "GSM2226360", "GSM2226361", "GSM2226362", "GSM2226363", "GSM2226364", "GSM2226365", "GSM2226366", "GSM2226367", "GSM2226368", "GSM2226369", "GSM2226370", "GSM2226371", "GSM2226372", "GSM2226373", "GSM2226374", "GSM2226375", "GSM2226376", "GSM2226377", "GSM2226378", "GSM2226379", "GSM2226380", "GSM2226381", "GSM2226382", "GSM2226383", "GSM2226384", "GSM2226385", "GSM2226386", "GSM2226387", "GSM2226388", "GSM2226389", "GSM2226390", "GSM2226391", "GSM2226392", "GSM2226393", "GSM2226394", "GSM2226395", "GSM2226396", "GSM2226397", "GSM2226398", "GSM2226399", "GSM2226400", "GSM2226401", "GSM2226402", "GSM2226403"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Characterization of gene expression profile in HBV-related liver fibrosis patients", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33859718:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:75b693c906c654a029945aeb5dc75492ea2701784cea10fd27e83df7b348c835", "bytes": 639, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tab1", "version": null, "note": "The summarized clinical characteristics of the 124 CHB patients.", "structure": {"pmcid": "PMC8028738", "section_index": 3, "section_title": "2.1. Collection of Gene Expression Data of HBV Patients", "row_count": 19, "column_count": 3}, "table": {"label": "Table 1", "caption": "The summarized clinical characteristics of the 124 CHB patients.", "rows": [["Clinical factor", "# of samples (n = 124)", "Ratio"], ["Gender"], ["Female", "36", "29.03%"], ["Male", "88", "70.97%"], ["Age"], ["<50 years", "92", "74.19%"], [">50 years", "32", "25.81%"], ["Scheuer score grading"], ["0", "37", "29.84%"], ["1", "33", "26.61%"], ["2", "34", "27.42%"], ["3", "15", "12.10%"], ["4", "5", "4.03%"], ["Scheuer score staging"], ["0", "43", "34.68%"], ["1", "20", "16.13%"], ["2", "33", "26.61%"], ["3", "18", "14.52%"], ["4", "10", "8.06%"]], "row_count": 19, "column_count": 3, "numeric_cells": 41, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tab1"}}], "gaps": ["asset:data:geo:GSE84044 not downloaded", "asset:data:geo:GSE84044 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The cell proportions between the groups were compared by the Wilcoxon-rank sum test. The gene expression data was obtained from Gene Expression Omnibus (GEO) with accession GSE84044 [26], which included 124 chronic hepatitis B (CHB) patients."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": "R1", "reachable": true, "accessions": ["GSE84044"], "resolved_accessions": ["GSE84044"], "statements": ["Previously reported gene expression and clinical data were used to support this study and are available at Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/gds). These prior studies (and datasets) are cited at relevant places within the text as references."], "basis": "The paper names GSE84044 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33859718", "data:geo:GSE84044", "asset:table:pmid:33859718:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84044"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:01Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25278, "completion_tokens": 930, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33859718", "type": "paper", "label": "pmid:33859718"}, {"id": "source:pmid:33859718", "type": "manuscript", "label": "PMID 33859718 full text"}, {"id": "data:geo:GSE84044", "type": "dataset", "label": "GEO GSE84044"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33859718", "type": "paper", "label": "pmid:33859718"}, {"id": "source:pmid:33859718", "type": "manuscript", "label": "PMID 33859718 full text"}, {"id": "data:geo:GSE84044", "type": "dataset", "label": "GEO GSE84044"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33859718", "type": "extraction", "used": ["source:pmid:33859718"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84044", "type": "accession_resolution", "used": ["data:geo:GSE84044"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33859718", "parent_hash": "sha256:97d0a467b7475d4e222ebf4de23058df33cda78f58c87d2541c949c09262b324", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE84044 licence not read", "asset:data:geo:GSE84044 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The cell proportions between the groups were compared by the Wilcoxon-rank sum test. The gene expression data was obtained from Gene Expression Omnibus (GEO) with accession GSE84044 [26], which included 124 chronic hepatitis B (CHB) patients."], "order_basis": "analysis_only", "id": "assay:1"}]}