Identification of 9 Gene Signatures by WGCNA to Predict Prognosis for Colon Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35392038", "kind": "science-record", "revision": 4, "content_hash": "sha256:8bf379317ee23af038132feb7d418f400b30c5f84601307c50441969f6d6a7f9", "created_at": "2026-11-01T18:14:12Z", "updated_at": "2026-11-01T22:06:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of 9 Gene Signatures by WGCNA to Predict Prognosis for Colon Adenocarcinoma.", "doi": "10.1155/2022/8598046", "pmid": "35392038", "authors": ["Mian Yang", "Haibin He", "Tao Peng", "Yi Lu", "Jiazi Yu"], "journal": "Computational intelligence and neuroscience", "year": 2022, "abstract": "Background: A risk assessment model for prognostic prediction of colon adenocarcinoma (COAD) was established based on weighted gene co-expression network analysis (WGCNA).\nMethods: From the Cancer Genome Atlas (TCGA) database, RNA-seq data and clinical data of COAD patients were retrieved. After screening of differentially expressed genes (DEGs), WGCNA was performed to identify gene modules and screen those associated with COAD progression. Then, via protein-protein interaction (PPI) network construction of module genes, hub genes were obtained, which were then subjected to the least absolute shrinkage and selection operator (LASSO) and Cox regression to build a hub gene-based prognostic scoring model. The receiver operating characteristic curve (ROC curve) was plotted for the optimal cutoff (OCO) of the risk score, based on which, patients were assigned to high or low-risk groups. Areas under the ROC curve (AUCs) were calculated, and model performance was visualized using Kaplan-Meier (KM) survival curves and verified in the external dataset GSE29621. Finally, the model's independent prognostic value was evaluated by univariate and multivariate Cox regression analyses, and a nomogram was built.\nResults: Totally 2840 DEGs were screened from COAD dataset of TCGA, including 1401 upregulated ones and 1439 downregulated ones, which were divided into 10 modules by WGCNA. The eigenvalue of the black module was found to have a high correlation with COAD progression. PPI interaction networks were constructed for genes in the black module, and 34 hub genes were obtained by using the MCODE plug-in. A LASSO-Cox regression approach was utilized to analyze the hub genes, and a prognostic risk score model based on the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) was constructed. KM analysis identified shorter overall lower survival in the high-risk group. The model was verified to have favorable predictive ability through training set and validation set. The nomogram, composed of tumor node metastasis (TNM) staging and risk score, was of good predictability.\nConclusions: The COAD prognostic risk model constructed upon the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) can effectively predict the survival status of COAD patients.", "claims": [{"id": "claim-method", "statement": "Using the WGCNA package of R, the DEGs were included in WGCNA to calculate the Pearson correlation coefficient between genes, and a feasible soft threshold β was chosen for ensuring SF network.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35392038", "locator": "sections[5] \"2.3. Weighted Gene Co-Expression Network Analysis (WGCNA)\" paragraph 2", "quote": "Using the WGCNA package of R, the DEGs were included in WGCNA to calculate the Pearson correlation coefficient between genes, and a feasible soft threshold β was chosen for ensuring SF network."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Previously reported bioinformatics data were used to support this study and are available at doi.org/10.1007/s11605-011-1815-0. These datasets are cited at relevant places within the text as references [14].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35392038", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "Previously reported bioinformatics data were used to support this study and are available at doi.org/10.1007/s11605-011-1815-0. These datasets are cited at relevant places within the text as references [14]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The COAD prognostic risk model constructed upon the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) can effectively predict the survival status of COAD patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35392038", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The COAD prognostic risk model constructed upon the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) can effectively predict the survival status of COAD patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The COAD prognostic risk model constructed upon the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) can effectively predict the survival status of COAD patients.", "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:35392038"], "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:GSE29621"], "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:GSE29621"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35392038", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/8598046", "sha256": "sha256:ea2eea3b08a1df602571e16cd1857a1afbf7026690ed28aee9ef536e1020d18a", "bytes": 37631, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/8598046", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8983226", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29621", "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=GSE29621", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29621", "version": null, "note": "Previously reported bioinformatics data were used to support this study and are available at doi.org/10.1007/s11605-011-1815-0. These datasets are cited at relevant places within the text as references [14].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Previously reported bioinformatics data were used to support this study and are available at doi.org/10.1007/s11605-011-1815-0. These datasets are cited at relevant places within the text as references [14].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM734111", "GSM734112", "GSM734113", "GSM734114", "GSM734115", "GSM734116", "GSM734117", "GSM734118", "GSM734119", "GSM734120", "GSM734121", "GSM734122", "GSM734123", "GSM734124", "GSM734125", "GSM734126", "GSM734127", "GSM734128", "GSM734129", "GSM734130", "GSM734131", "GSM734132", "GSM734133", "GSM734134", "GSM734135", "GSM734136", "GSM734137", "GSM734138", "GSM734139", "GSM734140", "GSM734141", "GSM734142", "GSM734143", "GSM734144", "GSM734145", "GSM734146", "GSM734147", "GSM734148", "GSM734149", "GSM734150", "GSM734151", "GSM734152", "GSM734153", "GSM734154", "GSM734155", "GSM734156", "GSM734157", "GSM734158", "GSM734159", "GSM734160", "GSM734161", "GSM734162", "GSM734163", "GSM734164", "GSM734165", "GSM734166", "GSM734167", "GSM734168", "GSM734169", "GSM734170", "GSM734171", "GSM734172", "GSM734173", "GSM734174", "GSM734175"], "sample_count": 65, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA and microRNA profile in colon cancer [mRNA data]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE29621 not downloaded", "asset:data:geo:GSE29621 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}, {"id": "method-6", "family": null, "specific": null, "label": "Weighted Gene Co-Expression Network Analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using the WGCNA package of R, the DEGs were included in WGCNA to calculate the Pearson correlation coefficient between genes, and a feasible soft threshold β was chosen for ensuring SF network."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE29621"], "resolved_accessions": ["GSE29621"], "statements": ["Previously reported bioinformatics data were used to support this study and are available at doi.org/10.1007/s11605-011-1815-0. These datasets are cited at relevant places within the text as references [14]."], "basis": "The paper names GSE29621 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:35392038", "data:geo:GSE29621"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29621"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:41:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11691, "completion_tokens": 1360, "cached_tokens": 264}}, "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:35392038", "type": "paper", "label": "pmid:35392038"}, {"id": "source:pmid:35392038", "type": "manuscript", "label": "PMID 35392038 full text"}, {"id": "data:geo:GSE29621", "type": "dataset", "label": "GEO GSE29621"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35392038", "type": "paper", "label": "pmid:35392038"}, {"id": "source:pmid:35392038", "type": "manuscript", "label": "PMID 35392038 full text"}, {"id": "data:geo:GSE29621", "type": "dataset", "label": "GEO GSE29621"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35392038", "type": "extraction", "used": ["source:pmid:35392038"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29621", "type": "accession_resolution", "used": ["data:geo:GSE29621"], "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:35392038", "parent_hash": "sha256:b8785d53a811a1ebe5121098ec025dbf5741187aabce2941269d9e684c4643b7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE29621 licence not read", "asset:data:geo:GSE29621 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "clinical_trial", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["off (OCO) of the risk score, based on which, patients were assigned to high or low-risk groups. Areas under the"], "order_basis": "paper_text_order:891", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}