Identification of Hub Genes in Liver Hepatocellular Carcinoma Based on Weighted Gene Co-expression Network Analysis.

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"structure": {"pmcid": "PMC12144059", "section_index": 17, "section_title": "Validation and Survival Analysis of Hub Genes and Expression of Hub Genes", "row_count": 21, "column_count": 4}, "table": {"label": "Table 1", "caption": "Expression of the Hub gene in LIHC and adjacent tissues from the ICGC database", "rows": [["Gene", "Type", "Expression log2(TPM + 1)", "P value"], ["CFP", "LIHC", "1.49 ± 0.89", "8.95E-98"], ["", "Adjacent", "3.89 ± 0.76", ""], ["CLEC1B", "LIHC", "0.59 ± 0.96", "4.41E-107"], ["", "Adjacent", "3.88 ± 1.05", ""], ["CLEC4G", "LIHC", "0.75 ± 1.18", "1.20E-125"], ["", "Adjacent", "4.71 ± 0.98", ""], ["CLEC4M", "LIHC", "0.52 ± 1.14", "8.52E-110"], ["", "Adjacent", "4.16 ± 1.10", ""], ["FCN2", "LIHC", "0.96 ± 1.30", "4.77E-115"], ["", "Adjacent", "4.90 ± 1.05", ""], ["FCN3", "LIHC", "2.091 ± 1.69", "1.03E-101"], ["", "Adjacent", "6.426 ± 1.13", ""], ["LYVE1", "LIHC", "1.26 ± 0.93", "1.95E-62"], ["", "Adjacent", "3.42 ± 1.10", ""], ["MARCO", "LIHC", "1.19 ± 1.42", "7.06E-80"], ["", "Adjacent", "4.88 ± 1.51", ""], ["PAMR1", "LIHC", "0.83 ± 0.63", "2.70E-61"], ["", "Adjacent", "2.10 ± 0.62", ""], ["TIMD4", "LIHC", "0.74 ± 0.84", "9.22E-40"], ["", "Adjacent", "2.23 ± 1.06", ""]], "row_count": 21, "column_count": 4, "numeric_cells": 31, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab1"}}], "gaps": ["asset:source:pmid:38683466 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38683466", "asset:table:pmid:38683466:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:38683466"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "cab09b32c9f3b7dc013ae92e08dda06b1680ec130454c3e45109f16e1a794c2d", "source_hash": "c5543b0a9f60402bf7df1dd7ab5b975f5ce4339811d78deade5acb6297ad3544", "raw_response_sha256": "sha256:cf25530157415649d118d166e060208b8030dcf44ff4be1bffbb56f6d102848a", "raw_response_chars": 5344}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "d46123099e394b9826ab22580c86378aa08a33b9ccd0a9348957ba8242b017a4", "source_hash": "c5543b0a9f60402bf7df1dd7ab5b975f5ce4339811d78deade5acb6297ad3544", "raw_response_sha256": "sha256:eac084492360e988a758ea7d53271f9179c1af09c51a17c938cac050624e3b50", "raw_response_chars": 47308}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "2e236c0fa3ce11d18a2782b240f67dff00920344a5214076ffd1a744dac2a43e", "source_hash": "c5543b0a9f60402bf7df1dd7ab5b975f5ce4339811d78deade5acb6297ad3544", "raw_response": "{\"parent_value\":10,\"unit\":\"hub genes\",\"evidence\":\"Then we demonstrated that the 10 hub genes (CFP, CLEC1B, CLEC4G, CLEC4M, FCN2, FCN3, PAMR1 and TIMD4) were weakly expressed in LIHC tissues\",\"target_result\":\"The paper states that 10 hub genes were identified and weakly expressed in LIHC tissues.\",\"number_stated\":true}", "reading": {"parent_value": 10, "unit": "hub genes", "evidence": "Then we demonstrated that the 10 hub genes (CFP, CLEC1B, CLEC4G, CLEC4M, FCN2, FCN3, PAMR1 and TIMD4) were weakly expressed in LIHC tissues", "target_result": "The paper states that 10 hub genes were identified and weakly expressed in LIHC tissues.", "number_stated": true, "source_locator": "chars 1484-1623 of source sha256 c5543b0a9f60402bf7df1dd7ab5b975f5ce4339811d78deade5acb6297ad3544"}, "recorded_at": "2026-10-31T15:17:20.577258+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "26f976103cf20c2b52187dec85120a164aaba3859e504d9ff92d2a615fb247d5", "source_hash": "c5543b0a9f60402bf7df1dd7ab5b975f5ce4339811d78deade5acb6297ad3544", "raw_response": "<think>We need answer JSON only. Need interpret registered target \"headline numerical result paper states for main finding\". Need single numerical result replication reproduce. Source abstract likely \"A total of 68 differential co-expression genes were extracted.\" This is headline numerical result main finding. Need value 68, unit perhaps \"differential co-expression genes\" (paper prints wording). Evidence exact contiguous quote containing number. \"A total of 68 differential co-expression genes were extracted.\" Unit must unit paper prints. Could unit be \"genes\" or \"differential co-expression genes\". Need target_result maybe describe. Asked headline number only perhaps JSON fields. parent_value number 68, unit \"differential co-expression genes\", evidence exact quote. target_result maybe \"The study extracted a total of 68 differential co-expression genes.\" But request report headline number only perhaps target_result should likely concise. Yet evidence required. Need exact quotation. Ensure no invented source. Could there be 10 hub genes as main finding? The title is identification hub genes. Abstract says \"Then we demonstrated that the 10 hub genes...\" But list has only 8 names due typo. Which is \"headline numerical result paper states for its main finding\"? Single numerical result a replication target. We need identify likely headline result. In abstract, central numerical outputs: 68 differential co-expression genes, 10 hub genes, six genes qRT-PCR downregulated, four associated OS/DFS, ten positive tumor purity. Registered target wording generic. \"headline numerical result the paper states for its main finding\" likely first result, 68 differential co-expression genes. Could unit be \"genes\". Let's parse user wording: They may expect extraction based on title and paper summary. They ask \"Read 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. The unit must be the unit the paper prints. ... Attribution may be carried by text's own wording: a number may be attached to target by a parenthetical list, by word respectively, or by words that name target directly. When that is how text links them, quote whole clause...\" This seems task perhaps identifies a target from title? Registered target = \"the headline numerical result the paper states for its main finding\". Need choose headline number in abstract. \"A total of 68 differential co-expression genes were extracted.\"</think>\n\n{\"parent_value\":68,\"unit\":\"differential co-expression genes\",\"evidence\":\"A total of 68 differential co-expression genes were extracted.\",\"target_result\":\"68 differential co-expression genes were extracted.\",\"number_stated\":true}", "reading": {"parent_value": 68, "unit": "differential co-expression genes", "evidence": "A total of 68 differential co-expression genes were extracted.", "target_result": "68 differential co-expression genes were extracted.", "number_stated": true, "source_locator": "chars 1186-1248 of source sha256 c5543b0a9f60402bf7df1dd7ab5b975f5ce4339811d78deade5acb6297ad3544"}, "recorded_at": "2026-10-31T15:17:20.809439+00:00"}], "agreement": false, "disagreements": {"physical_methods": {"minimax": ["qRT-PCR"], "minimax_alt": ["qRT-PCR of clinical samples"], "decisive": false}, "analysis_methods": {"minimax": ["Weighted Gene Co-expression Network Analysis (WGCNA)", "differential gene expression analysis", "Genetic Ontology (GO) enrichment analysis", "Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis", "protein-protein interaction (PPI) network validation", "GEPIA2 expression analysis", "Kaplan-Meier survival analysis", "TIMER immune-infiltration analysis"], "minimax_alt": ["Weighted Gene Co-expression Network Analysis (WGCNA)", "differential gene expression analysis", "Gene Ontology (GO) enrichment analysis", "Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis", "protein-protein interaction (PPI) network analysis", "GEPIA2 expression and survival analysis", "Kaplan-Meier survival analysis", "Tumor Immune Estimation Resource (TIMER) immune infiltration analysis"], "decisive": false}, "statistical_method": {"minimax": "Weighted Gene Co-expression Network Analysis (WGCNA)", "minimax_alt": "Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis methods", "decisive": true}, "parent_value": {"minimax": 10, "minimax_alt": 68, "decisive": true}, "unit": {"minimax": "hub genes", "minimax_alt": "differential co-expression genes", "decisive": true}}, "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": "blocked", "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.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:9bb00a5ad9385bfc151d20db3f0e21c124c89d2c8a682455e7be0f568d397601", "type": "sep_package", "label": "SEP v1 package for pmid:38683466"}], "activities": [{"id": "activity:conversion:pmid:38683466", "type": "conversion", "used": ["package:9bb00a5ad9385bfc151d20db3f0e21c124c89d2c8a682455e7be0f568d397601"], "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:38683466", "parent_hash": "sha256:72ed66b16c531df908dbc20b3e5835f585874d64b74d3733efcd7355555bdbe5", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:38683466 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "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:38683466' does not resolve to a declared asset", "targets"]}