Bioinformatics Analysis Screening and Identification of Key Biomarkers and Drug Targets in Human Glioblastoma.

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"Sarcolemma", "3", "0.022842198"], ["GO:0005737", "Cytoplasm", "22", "0.022951589"]], "row_count": 11, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[9]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:39248068:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27e684c3ef085707f30b0654d4d2d187c5403092956ad700e32d0a6a10d6309f", "bytes": 880, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[3]#T3", "version": null, "note": "Changes in cell component (CC) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 9, "section_title": "KEGG and GO Enrichment Analyses of DEGs", "row_count": 12, "column_count": 4}, "table": {"label": "Table 3", "caption": "Changes in cell component (CC) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "rows": [["Term", "Description", "Count in Gene Set", "p-value"], ["cfa04510:", "Focal adhesion", "6", "0.003963"], ["cfa04151:", "PI3K-Akt signaling pathway", "7", "0.007034"], ["cfa04974:", "Protein digestion and absorption", "4", "0.009134"], ["cfa04512:", "ECM-receptor interaction", "4", "0.010054"], ["cfa05146:", "Amoebiasis", "4", "0.017115"], ["cfa05205:", "Proteoglycans in cancer", "5", "0.017563"], ["cfa04114:", "Oocyte meiosis", "4", "0.017985"], ["cfa04110:", "Cell cycle", "4", "0.025292"], ["cfa05206:", "MicroRNAs in cancer", "4", "0.034612"], ["cfa04115:", "p53 signaling pathway", "3", "0.044317"], ["cfa05200:", "Pathways in cancer", "6", "0.048794"]], "row_count": 12, "column_count": 4, "numeric_cells": 34, "header_rows": 1, "locator": "section[9]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:39248068:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:07d9dade77d8ed6c52afc1821c6d708be9a423462b5a847667802ca24a6e51ff", "bytes": 814, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[4]#T4", "version": null, "note": "Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 9, "section_title": "KEGG and GO Enrichment Analyses of DEGs", "row_count": 9, "column_count": 4}, "table": {"label": "Table 4", "caption": "Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) in glioblastoma.", "rows": [["Term", "Pathway Description", "Count", "p-value"], ["GO:0003777", "Microtubule motor activity", "5", "2.36E-04"], ["GO:0005201", "Extracellular matrix structural constituent", "4", "9.42E-04"], ["GO:0016887", "ATPase activity", "5", "0.001533"], ["GO:0005524", "ATP binding", "14", "0.005736"], ["GO:0035174", "Histone serine kinase activity", "2", "0.025983"], ["GO:0004871", "Signal transducer activity", "4", "0.026153"], ["GO:0005200", "Structural constituent of cytoskeleton", "3", "0.028268"], ["GO:0004859", "Phospholipase inhibitor activity", "2", "0.031099"]], "row_count": 9, "column_count": 4, "numeric_cells": 24, "header_rows": 1, "locator": "section[9]/table-wrap[4]#T4"}}, {"id": "asset:table:pmid:39248068:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a9dbe32eb4ce1e52a2ba606676c3958b70e0cc35417ac2985fc5e793d4b95077", "bytes": 4946, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T5", "version": null, "note": "Functional roles of 27 hub genes with degree-10.", "structure": {"pmcid": "PMC12606603", "section_index": 11, "section_title": "Hub Gene Selection and Analysis", "row_count": 28, "column_count": 3}, "table": {"label": "Table 5", "caption": "Functional roles of 27 hub genes with degree-10.", "rows": [["Gene Symbol", "Full Name", "Function"], ["GINS1", "DNA replication complex GINS protein PSF1", "The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks."], ["SKA1", "Spindle and kinetochore-associated protein 1", "Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation."], ["BUB1B", "Mitotic checkpoint serine/threonine-protein kinase BUB1 beta", "Essential component of the mitotic checkpoint. Required for normal mitosis progression."], ["CCNB2", "G2/mitotic-specific cyclin-B2", "CCNB2 (cyclin B2) is associated with invasion, metastasis and poor prognosis of several cancers."], ["MELK", "Maternal embryonic leucine zipper kinase", "Serine/threonine-protein kinase involved in various processes such as cell cycle regulation, self-renewal of stem cells, apoptosis and splicing regulation."], ["KIAA0101", "PCNA-associated factor", "PCNA-binding protein that acts as a regulator of DNA repair during DNA replication."], ["SHCBP1", "SHC SH2 domain-binding protein 1", "May play a role in signaling pathways governing cellular proliferation, cell growth and differentiation."], ["AURKB", "Aurora kinase B", "Serine/threonine-protein kinase component of the chromosomal passenger complex (CPC), a complex that acts as a key regulator of mitosis."], ["EZH2", "Histone-lysine N-methyltransferase EZH2", "Catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys- 27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene."], ["KNTC1", "Kinetochore-associated protein 1", "Essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis."], ["SMC4", "Structural maintenance of chromosomes protein 4", "Central component of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes."], ["RRM2", "Ribonucleoside-diphosphate reductase subunit M2", "Provides the precursors necessary for DNA synthesis."], ["KIF14", "Kinesin-like protein KIF14", "Microtubule motor protein that binds to microtubules with high affinity through each tubulin heterodimer and has an ATPase activity (By similarity)."], ["LMNB1", "Lamin-B1", "Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin."], ["CENPN", "Centromere protein N", "Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation."], ["KIFC1", "Kinesin-like protein KIFC1", "Minus end-directed microtubule-dependent motor required for bipolar spindle formation."], ["KIF20A", "Kinesin-like protein KIF20A", "Mitotic kinesin required for chromosome passenger complex (CPC)-mediated cytokinesis."], ["CEP55", "Centrosomal protein of 55 kDa", "Plays a role in mitotic exit and cytokinesis."], ["TOP2A", "Topoisomerase(DNA)II ɑ", "Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands."], ["NUSAP1", "Nucleolar and spindle associated protein 1", "High expression of NUSAP1 is involved in the progression of prostate cancer."], ["CDK1", "Cyclin-dependent kinase 1", "Plays a key role in the control of the eukaryotic cell cycle by modulating the centrosome cycle as well as mitotic onset."], ["ASPM", "Abnormal spindle-like microcephaly-associated protein", "The function in regulating microtubule dynamics at spindle poles including spindle orientation, astral microtubule density and poleward microtubule flux seems to depend on the association with the katanin complex formed by KATNA1 and KATNB1."], ["AURKA", "Aurora kinase A", "Mitotic serine/threonine kinase that contributes to the regulation of cell cycle progression."], ["NCAPG", "Activation of CDK1 at centrosomes", "Regulatory subunit of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes."], ["GINS2", "DNA replication complex GINS protein PSF2", "The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks."], ["KIF23", "Kinesin-like protein KIF23", "Component of the centralspindlin complex that serves as a microtubule-dependent and Rho-mediated signaling required for the myosin contractile ring formation during the cell cycle cytokinesis."], ["NDC80", "Kinetochore protein NDC80 homolog", "Acts as a component of the essential kinetochore- associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity."]], "row_count": 28, "column_count": 3, "numeric_cells": 19, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:39248068:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fed30ad285e2a858745b5b1d4fdc1acec7f15c859d2352f0277cac27440be4dd", "bytes": 890, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T6", "version": null, "note": "Biological processes (BP) pathway enrichment analysis of hub genes in glioblastoma.", "structure": {"pmcid": "PMC12606603", "section_index": 11, "section_title": "Hub Gene 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"raw_response": "{\"parent_value\":88,\"unit\":\"DEGs\",\"evidence\":\"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\",\"target_result\":\"The paper reports that the analysis identified 88 differentially expressed genes.\",\"number_stated\":true}", "reading": {"parent_value": 88, "unit": "DEGs", "evidence": "The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.", "target_result": "The paper reports that the analysis identified 88 differentially expressed genes.", "number_stated": true, "source_locator": "chars 1600-1686 of source sha256 c0dcbf60d04ef0239605a4f44d14bbf384886b7de824ce757251bcd342225a98"}, "recorded_at": "2026-10-31T15:18:37.408112+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e2a54b8528cd10ab52e8a843794c4cc074f95f00336b2401c22c1218aab696ea", "source_hash": "c0dcbf60d04ef0239605a4f44d14bbf384886b7de824ce757251bcd342225a98", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result main finding. Paper main finding: identified 88 DEGs and 27 central hub genes. User asks single numerical result headline number paper itself states for registered target \"the headline numerical result the paper states for its main finding\". Need decide 88 likely headline numerical result, perhaps 27 key genes? They demand single numerical result. Need parse language. Abstract: \"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes... A group of 27 pivotal genes...\" Main headline perhaps 88 DEGs. Conclusion: \"we identified 88 DEGs and pinpointed 27 central hub genes\". Which is \"headline numerical result\" singular? Likely expected number 88, unit \"DEGs\". Evidence exact contiguous quote containing number. Could quote: \"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\" This directly attributes 88 to DEGs and exact quote. unit printed likely \"DEGs\". target_result maybe \"The analysis yielded 88 DEGs.\" Need JSON parent_value 88, unit \"DEGs\", evidence exact sentence. number_stated true.\n\nBut ambiguity: Main finding might be \"27 central hub genes\" due title key biomarkers and drug targets, registered target says headline numerical result paper states for its main finding. Need infer benchmark conventions. They likely ask extraction of a single numerical result from paper, perhaps target label generated from paper metadata? The source is likely abstract converted. The headline numerical result often \"88 DEGs\" because first result. Yet main finding could be 27 hub genes. Let's deeply assess.\n\nPrompt: \"Read the supplied paper text and find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed.\" Registered target: \"the headline numerical result the paper states for its main finding\". We need pick headline number. Abstract Results first sentence 88 DEGs. Then breakdown 66 and 22. \"A group of 27 pivotal genes\". Conclusion emphasizes \"identified 88 DEGs and pinpointed 27 central hub genes\". Paper's main finding can involve both. But asks single headline number likely 88 DEGs, because \"headline numerical result\" and unit. Maybe target is intentionally generic and need determine. Could perhaps select 27 as number of key genes identified, because title screening/identification key biomarkers/drug targets and final conclusion says \"Through our analysis, we identified 88 DEGs and pinpointed 27 central hub genes, which hold the potential to serve as diagnostic markers\". Which is headline? Both. Yet instruction says single. Usually in benchmark, registered target might be something like \"88 differentially expressed genes\" but they've paraphrased target vaguely? They explicitly label \"REGISTERED TARGET: the headline numerical result the paper states for its main finding.\" Maybe expected to identify most headline statistic. Need choose.\n\nLet's inspect source title \"Bioinformatics Analysis Screening and Identification of Key Biomarkers and Drug Targets in Human Glioblastoma\". Abstract likely from paper (Iranian Journal?). Typical abstract results: \"The analysis yielded 88 DEGs... A group of 27 pivotal genes was pinpointed...\" The headline numerical result may be 88 DEGs, perhaps because they ask a replication has to reproduce, registered target is \"the headline numerical result ...\". The first quantitative result is 88. Unit as printed \"DEGs\". Evidence must exact contiguous quote. If choose 88, evidence sentence.\n\nNeed output JSON object only. Ensure valid JSON, no markdown. target_result can explain \"The analysis yielded 88 DEGs.\" Or perhaps \"88 differentially expressed genes (DEGs).\" Unit must printed unit: \"DEGs\". The instruction \"Report the headline number only\" likely target_result should perhaps be concise. Could set target_result \"The paper reports 88 DEGs as the main analysis result.\" Evidence full clause. number_stated true.\n\nLet's ensure evidence exact contiguous source quote: \"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\" Yes exact. Unit \"DEGs\". parent_value 88. JSON.</think>\n\n{\"parent_value\":88,\"unit\":\"DEGs\",\"evidence\":\"The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.\",\"target_result\":\"The paper reports 88 differentially expressed genes as the headline result.\",\"number_stated\":true}", "reading": {"parent_value": 88, "unit": "DEGs", "evidence": "The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes.", "target_result": "The paper reports 88 differentially expressed genes as the headline result.", "number_stated": true, "source_locator": "chars 1600-1686 of source sha256 c0dcbf60d04ef0239605a4f44d14bbf384886b7de824ce757251bcd342225a98"}, "recorded_at": "2026-10-31T15:18:29.102705+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "The analysis yielded 88 DEGs, consisting of 66 upregulated and 22 downregulated genes, and 27 pivotal hub genes were identified.", "minimax_alt": "The analysis yielded 88 differentially expressed genes (66 upregulated and 22 downregulated) and pinpointed 27 pivotal hub genes.", "decisive": false}, "analysis_methods": {"minimax": ["microarray analysis", "differentially expressed gene identification", "function enrichment analysis", "STRING protein-protein interaction network construction", "MCODE module analysis", "hub gene selection by connectivity degree", "hierarchical clustering", "Kaplan-Meier curve analyses"], "minimax_alt": ["Microarray analysis", "Differentially expressed gene (DEG) identification", "Function enrichment analysis", "Protein-protein interaction network construction using STRING version 10.0, with a combined interaction score greater than 0.4", "Molecular Complex Detection (MCODE) module analysis using Cytoscape version 3.4.0, with an MCODE score exceeding 5, degree cut-off of 2, node score cut-off of 0.2, maximum depth of 100, and k-score of 2", "DAVID functional enrichment analysis", "Hub-gene selection based on connectivity degrees of 10 or higher", "BiNGO biological-process analysis in Cytoscape", "Hierarchical clustering using the UCSC Cancer Genomics Browser"], "decisive": false}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "passed", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:b6ae32827a9f340bbbc8e2537984988fa094fdc752770bbc21bf8d38621e2865", "type": "sep_package", "label": "SEP v1 package for pmid:39248068"}], "activities": [{"id": "activity:conversion:pmid:39248068", "type": "conversion", "used": ["package:b6ae32827a9f340bbbc8e2537984988fa094fdc752770bbc21bf8d38621e2865"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39248068", "parent_hash": "sha256:7ee0a1f820ebfefa1c710ab9d229744e27b71b5e6b67ac1b200bb15dbb80622b", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39248068 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39248068' does not resolve to a declared asset", "targets"]}