Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36317111", "kind": "science-record", "revision": 4, "content_hash": "sha256:94fbe4ca06bbec4908a7215820ff0db6f0c979d6879a5bb2fae195eef3ab195c", "created_at": "2026-11-01T18:15:44Z", "updated_at": "2026-11-01T22:50:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis.", "doi": "10.1155/2022/4237633", "pmid": "36317111", "authors": ["Mohib Ullah Kakar", "Muhammad Zubair Mehboob", "Muhammad Akram", "Muddaser Shah", "Yasmeen Shakir", "Hafza Wajeeha Ijaz", "Ubair Aziz", "Zahid Ullah", "Sajjad Ahmad", "Sikandar Ali", "Yongxiang Yin"], "journal": "BioMed research international", "year": 2022, "abstract": "Objective: The goal of this study was to understand the possible core genes associated with hepatocellular carcinoma (HCC) pathogenesis and prognosis.\nMethods: GEO contains datasets of gene expression, miRNA, and methylation patterns of diseased and healthy/control patients. The GSE62232 dataset was selected by employing the server Gene Expression Omnibus. A total of 91 samples were collected, including 81 HCC and 10 healthy samples as control. GSE62232 was analysed through GEO2R, and Functional Enrichment Analysis was performed to extract rational information from a set of DEGs. The Protein-Protein Relationship Networking search method has been used for extracting the interacting genes. MCC method was used to calculate the top 10 genes according to their importance. Hub genes in the network were analysed using GEPIA to estimate the effect of their differential expression on cancer progression.\nResults: We identified the top 10 hub genes through CytoHubba plugin. These included BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1 and MAD2L1, NCAPG, and NDC80. NCAPG and NDC80 reported for the first time in this study while the remaining from a recently reported literature. The pathogenesis of HCC may be directly linked with the aforementioned genes. In this analysis, we found critical genes for HCC that showed recommendations for future prognostic and predictive biomarkers studies that could promote selective molecular therapy for HCC.", "claims": [{"id": "claim-method", "statement": "To evaluate the overall prognostic importance of hub genes in this study, Kaplan-Meier survival analysis was performed to examine the association between different expression levels of genes and survival time of patients with HCC. The logrank p value was estimated, where p value smaller than 0.05 indicates a statistically significant difference in mortality between the high-level and low-level groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36317111", "locator": "sections[6] \"2.4. Survival Analysis through GEPIA and Expression Level of Hub Genes\" paragraph 2", "quote": "To evaluate the overall prognostic importance of hub genes in this study, Kaplan-Meier survival analysis was performed to examine the association between different expression levels of genes and survival time of patients with HCC. The logrank p value was estimated, where p value smaller than 0.05 indicates a statistically significant difference in mortality between the high-level and low-level groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We collected raw data of GSE62232 from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62232. It is an online repository, and data can be accessed directly from the study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36317111", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "We collected raw data of GSE62232 from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62232. It is an online repository, and data can be accessed directly from the study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 10 hub genes associated with hepatocellular carcinoma: BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1, MAD2L1, NCAPG, and NDC80.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36317111", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified the top 10 hub genes through CytoHubba plugin. These included BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1 and MAD2L1, NCAPG, and NDC80."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 10 hub genes associated with hepatocellular carcinoma: BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1, MAD2L1, NCAPG, and NDC80.", "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:36317111"], "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:GSE62232"], "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": {"p_value": "analysis with a logrank p value"}, "inputs": ["data:geo:GSE62232"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36317111", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/4237633", "sha256": "sha256:7ea68f5e047b63f6aa35f1c013e21756537b3cf0cc3fac7cb0720e337eb4df07", "bytes": 25758, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/4237633", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9617698", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62232", "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=GSE62232", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62232", "version": null, "note": "We collected raw data of GSE62232 from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62232. It is an online repository, and data can be accessed directly from the study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We collected raw data of GSE62232 from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62232. It is an online repository, and data can be accessed directly from the study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1523329", "GSM1523330", "GSM1523331", "GSM1523332", "GSM1523333", "GSM1523334", "GSM1523335", "GSM1523336", "GSM1523337", "GSM1523338", "GSM1523339", "GSM1523340", "GSM1523341", "GSM1523342", "GSM1523343", "GSM1523344", "GSM1523345", "GSM1523346", "GSM1523347", "GSM1523348", "GSM1523349", "GSM1523350", "GSM1523351", "GSM1523352", "GSM1523353", "GSM1523354", "GSM1523355", "GSM1523356", "GSM1523357", "GSM1523358", "GSM1523359", "GSM1523360", "GSM1523361", "GSM1523362", "GSM1523363", "GSM1523364", "GSM1523365", "GSM1523366", "GSM1523367", "GSM1523368", "GSM1523369", "GSM1523370", "GSM1523371", "GSM1523372", "GSM1523373", "GSM1523374", "GSM1523375", "GSM1523376", "GSM1523377", "GSM1523378", "GSM1523379", "GSM1523380", "GSM1523381", "GSM1523382", "GSM1523383", "GSM1523384", "GSM1523385", "GSM1523386", "GSM1523387", "GSM1523388", "GSM1523389", "GSM1523390", "GSM1523391", "GSM1523392", "GSM1523393", "GSM1523394", "GSM1523395", "GSM1523396", "GSM1523397", "GSM1523398", "GSM1523399", "GSM1523400", "GSM1523401", "GSM1523402", "GSM1523403", "GSM1523404", "GSM1523405", "GSM1523406", "GSM1523407", "GSM1523408", "GSM1523409", "GSM1523410", "GSM1523411", "GSM1523412", "GSM1523413", "GSM1523414", "GSM1523415", "GSM1523416", "GSM1523417", "GSM1523418", "GSM1523419"], "sample_count": 91, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Large-scale gene expression profiling  of 81 hepatocellular carcinomas", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE62232 not downloaded", "asset:data:geo:GSE62232 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "analysis with a logrank p value"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To evaluate the overall prognostic importance of hub genes in this study, Kaplan-Meier survival analysis was performed to examine the association between different expression levels of genes and survival time of patients with HCC. 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