Identification of a key glioblastoma candidate gene, FUBP3, based on weighted gene co-expression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35413821", "kind": "science-record", "revision": 4, "content_hash": "sha256:b84b8c79e439117aa605ce3965eb59c0494c3c6bf55156ab15d20c673fa47c48", "created_at": "2026-11-01T18:14:14Z", "updated_at": "2026-11-01T22:06:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a key glioblastoma candidate gene, FUBP3, based on weighted gene co-expression network analysis.", "doi": "10.1186/s12883-022-02661-x", "pmid": "35413821", "authors": ["Jianmin Li", "Zhao Zhang", "Ke Guo", "Shuhua Wu", "Chong Guo", "Xinfan Zhang", "Zi Wang"], "journal": "BMC neurology", "year": 2022, "abstract": "BACKGROUND: Glioblastoma multiforme (GBM) is the most common aggressive malignant brain tumor. However, the molecular mechanism of glioblastoma formation is still poorly understood. To identify candidate genes that may be connected to glioma growth and development, weighted gene co-expression network analysis (WGCNA) was performed to construct a gene co-expression network between gene sets and clinical characteristics. We also explored the function of the key candidate gene.\nMETHODS: Two GBM datasets were selected from GEO Datasets. The R language was used to identify differentially expressed genes. WGCNA was performed to construct a gene co-expression network in the GEO glioblastoma samples. A custom Venn diagram website was used to find the intersecting genes. The GEPIA website was applied for survival analysis to determine the significant gene, FUBP3. OS, DSS, and PFI analyses, based on the UCSC Cancer Genomics Browser, were performed to verify the significance of FUBP3. Immunohistochemistry was performed to evaluate the expression of FUBP3 in glioblastoma and adjacent normal tissue. KEGG and GO enrichment analyses were used to reveal possible functions of FUBP3. Microenvironment analysis was used to explore the relationship between FUBP3 and immune infiltration. Immunohistochemistry was performed to verify the results of the microenvironment analysis.\nRESULTS: GSE70231 and GSE108474 were selected from GEO Datasets, then 715 and 694 differentially expressed genes (DEGs) from GSE70231 and GSE108474, respectively, were identified. We then performed weighted gene co-expression network analysis (WGCNA) and identified the most downregulated gene modules of GSE70231 and GSE108474, and 659 and 3915 module genes from GSE70231 and GSE108474, respectively, were selected. Five intersection genes (FUBP3, DAD1, CLIC1, ABR, and DNM1) were calculated by Venn diagram. FUBP3 was then identified as the only significant gene by survival analysis using the GEPIA website. OS, DSS, and PFI analyses verified the significance of FUBP3. Immunohistochemical analysis revealed FUBP3 expression in GBM and adjacent normal tissue. KEGG and GO analyses uncovered the possible function of FUBP3 in GBM. Tumor microenvironment analysis showed that FUBP3 may be connected to immune infiltration, and immunohistochemistry identified a positive correlation between immune cells (CD4 + T cells, CD8 + T cells, and macrophages) and FUBP3.\nCONCLUSION: FUBP3 is associated with immune surveillance in GBM, indicating that it has a great impact on GBM development and progression. Therefore, interventions involving FUBP3 and its regulatory pathway may be a new approach for GBM treatment.", "claims": [{"id": "claim-data-access", "statement": "RNA sequence data from human glioblastoma samples (GSE70231 and GSE108474) were obtained from GEO datasets (http://www.ncbi.nlm.nih.gov/geo/).Venn diagram website (http://bioinformatics.psb.ugent.be/webtools/Venn/).GEPIA website (http://gepia.cancer-pku.cn/).UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu).GSEA’s official website (https://www.gsea-msigdb.org/gsea/register.jsp).TIMER webserver (https://cistrome.shinyapps.io/timer/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35413821", "locator": "sections[27] \"notes\" paragraph 1", "quote": "RNA sequence data from human glioblastoma samples (GSE70231 and GSE108474) were obtained from GEO datasets (http://www.ncbi.nlm.nih.gov/geo/).Venn diagram website (http://bioinformatics.psb.ugent.be/webtools/Venn/).GEPIA website (http://gepia.cancer-pku.cn/).UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu).GSEA’s official website (https://www.gsea-msigdb.org/gsea/register.jsp).TIMER webserver (https://cistrome.shinyapps.io/timer/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "FUBP3 is associated with immune surveillance in GBM, indicating that it has a great impact on GBM development and progression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35413821", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "FUBP3 is associated with immune surveillance in GBM, indicating that it has a great impact on GBM development and progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "FUBP3 is associated with immune surveillance in GBM, indicating that it has a great impact on GBM development and progression.", "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:35413821"], "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:GSE108474"], "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:GSE108474"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35413821", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12883-022-02661-x", "sha256": "sha256:ffcad326858ed11db910ffa4fbef1f06b3a05586b15d60aa99a83577f880af34", "bytes": 33026, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12883-022-02661-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9004042", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE108474", "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=GSE108474", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108474", "version": null, "note": "RNA sequence data from human glioblastoma samples (GSE70231 and GSE108474) were obtained from GEO datasets (http://www.ncbi.nlm.nih.gov/geo/).Venn diagram website (http://bioinformatics.psb.ugent.be/webtools/Venn/).GEPIA website (http://gepia.cancer-pku.cn/).UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu).GSEA’s official website (https://www.gsea-msigdb.org/gsea/register.jsp).TIMER webserver (https://cistrome.shinyapps.io/timer/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA sequence data from human glioblastoma samples (GSE70231 and GSE108474) were obtained from GEO datasets (http://www.ncbi.nlm.nih.gov/geo/).Venn diagram website (http://bioinformatics.psb.ugent.be/webtools/Venn/).GEPIA website (http://gepia.cancer-pku.cn/).UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu).GSEA’s official website (https://www.gsea-msigdb.org/gsea/register.jsp).TIMER webserver (https://cistrome.shinyapps.io/timer/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2899178", 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