Long noncoding RNAs predict the survival of patients with colorectal cancer as revealed by constructing an endogenous RNA network using bioinformation analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30714675", "kind": "science-record", "revision": 9, "content_hash": "sha256:ae0988bb5809696b802418b43fec09fdf66b52283478633e0dbed85ead5cae0e", "created_at": "2026-11-01T15:40:41Z", "updated_at": "2026-11-01T22:43:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Long noncoding RNAs predict the survival of patients with colorectal cancer as revealed by constructing an endogenous RNA network using bioinformation analysis.", "doi": "10.1002/cam4.1813", "pmid": "30714675", "authors": ["Hui Zhang", "Zhuo Wang", "Jianzhong Wu", "Rong Ma", "Jifeng Feng"], "journal": "Cancer medicine", "year": 2019, "abstract": "Long noncoding RNAs (lncRNAs) are aberrantly expressed in various cancers types and can function as competing endogenous RNAs (ceRNAs), which promote and maintain tumor initiation and progression. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in colorectal cancer and their clinical potential as biomarkers. The RNA sequencing profiles of patients with colorectal cancer were downloaded from TCGA database, and 62 lncRNAs, 30miRNAs, and 59 mRNAs were identified to comprise the ceRNA network (fold change > 2, P < 0.01). Functional enrichment analysis suggested that the target genes of the ceRNA network may be involved in the pathways related to cancer, including the signaling pathway that regulates the pluripotency of stem cells, wnt signaling pathway, hippo signaling pathway, basal cell carcinoma, and colorectal cancer. Univariate and multivariate Cox's proportional hazard regression model revealed that five (H19, MIR31HG, HOTAIR, WT1-AS, and LINC00488) out of 62 lncRNAs were closely related to the overall survival (OS) (P < 0.05). Furthermore, the five-lncRNA model could be an independent prognostic model in colorectal cancer. We computed for the risk function and constructed a risk score based on the five lncRNAs. Results showed that patients with high-risk scores have poor survival rates. Additionally, combing the risk score and other clinicopathological features, we can better predict the patient's survival probabilities. Furthermore, we validate our model in the GSE38832 dataset. Collectively, our study has provided a deeper understanding of the lncRNA-related ceRNA regulatory mechanism in CRC and identified five-lncRNA model, which could be considered as candidate prognostic biomarkers and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The DERNA (DElncRNAs, DEmRNAs, and DEmiRNAs) data between tumor and normal samples were analyzed using “edgeR” package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30714675", "locator": "sections[4] \"Screening of differentially expressed RNAs (DERNAs)\" paragraph 2", "quote": "The DERNA (DElncRNAs, DEmRNAs, and DEmiRNAs) data between tumor and normal samples were analyzed using “edgeR” package in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA‐Seq data and clinical information of CRC patients were completely downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30714675", "locator": "sections[3] \"Patient information and data processing\" paragraph 2", "quote": "The RNA‐Seq data and clinical information of CRC patients were completely downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30714675"], "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:GSE38832"], "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:GSE38832"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30714675", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.1813", "sha256": "sha256:eb444f2fdbce3de9c7f22db008f3eca56d25dbdc0aa22b142c034bd2a545a867", "bytes": 29357, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.1813", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6434209", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE38832", "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=GSE38832", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38832", "version": null, "note": "The RNA‐Seq data and clinical information of CRC patients were completely downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA‐Seq data and clinical information of CRC patients were completely downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM950411", "GSM950412", "GSM950413", "GSM950414", "GSM950415", "GSM950416", "GSM950417", "GSM950418", "GSM950419", "GSM950420", "GSM950421", "GSM950422", "GSM950423", "GSM950424", "GSM950425", "GSM950426", "GSM950427", "GSM950428", "GSM950429", "GSM950430", "GSM950431", "GSM950432", "GSM950433", "GSM950434", "GSM950435", "GSM950436", "GSM950437", "GSM950438", "GSM950439", "GSM950440", "GSM950441", "GSM950442", "GSM950443", "GSM950444", "GSM950445", "GSM950446", "GSM950447", "GSM950448", "GSM950449", "GSM950450", "GSM950451", "GSM950452", "GSM950453", "GSM950454", "GSM950455", "GSM950456", "GSM950457", "GSM950458", "GSM950459", "GSM950460", "GSM950461", "GSM950462", "GSM950463", "GSM950464", "GSM950465", "GSM950466", "GSM950467", "GSM950468", "GSM950469", "GSM950470", "GSM950471", "GSM950472", "GSM950473", "GSM950474", "GSM950475", "GSM950476", "GSM950477", "GSM950478", "GSM950479", "GSM950480", "GSM950481", "GSM950482", "GSM950483", "GSM950484", "GSM950485", "GSM950486", "GSM950487", "GSM950488", "GSM950489", "GSM950490", "GSM950491", "GSM950492", "GSM950493", "GSM950494", "GSM950495", "GSM950496", "GSM950497", "GSM950498", "GSM950499", "GSM950500", "GSM950501", "GSM950502", "GSM950503", "GSM950504", "GSM950505", "GSM950506", "GSM950507", "GSM950508", "GSM950509", "GSM950510", "GSM950511", "GSM950512", "GSM950513", "GSM950514", "GSM950515", "GSM950516", "GSM950517", "GSM950518", "GSM950519", "GSM950520", "GSM950521", "GSM950522", "GSM950523", "GSM950524", "GSM950525", "GSM950526", "GSM950527", "GSM950528", "GSM950529", "GSM950530", "GSM950531", "GSM950532"], "sample_count": 122, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "NFAT transcriptional activity is associated with metastatic capacity in colon cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30714675:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:30617f8fe592ae9b2884cea024809cb9f837d8ed90fe6ba5d85b2f2457fe707c", "bytes": 637, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#cam41813-tbl-0001", "version": null, "note": "Overall information on the five prognostic lncRNAs", "structure": {"pmcid": "PMC6434209", "section_index": 7, "section_title": "Building a predictive model for prognosis and survival", "row_count": 7, "column_count": 6}, "table": {"label": "Table 1", "caption": "Overall information on the five prognostic lncRNAs", "rows": [["DElncRNAs", "Ensembl ID", "Univariate analysis", "Multivariate analysis"], ["HR", "P value", "HR", "P value"], ["H19", "ENSG00000130600", "1.098", "0.008**", "1.079", "0.038*"], ["MIR31HG", "ENSG00000171889", "0.821", "0.033*", "1.184", "0.025*"], ["HOTAIR", "ENSG00000228630", "1.111", "0.005**", "1.094", "0.019*"], ["WT1‐AS", "ENSG00000183242", "1.112", "0.034*", "1.103", "0.041*"], ["LINC00488", "ENSG00000214381", "0.754", "0.048*", "0.856", "0.106"]], "row_count": 7, "column_count": 6, "numeric_cells": 28, "header_rows": 2, "locator": "section[15]/table-wrap[1]#cam41813-tbl-0001"}}, {"id": "asset:table:pmid:30714675:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:80995975179e0e752896b2f681f7b5e00859f2bd8e59f91abe6164009633dfe7", "bytes": 874, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#cam41813-tbl-0002", "version": null, "note": "The correlations between the five‐lncRNA model and clinical features", "structure": {"pmcid": "PMC6434209", "section_index": 9, "section_title": "Combining risk score with clinical significance prognostic prediction for CRC", "row_count": 23, "column_count": 5}, "table": {"label": "Table 2", "caption": "The correlations between the five‐lncRNA model and clinical features", "rows": [["Variable", "Number", "Risk score"], ["Low risk", "High risk", "P value"], ["Age"], ["≤65", "251", "132", "119", "0.293"], ["＞65", "316", "151", "165", ""], ["Gender"], ["Male", "254", "133", "121", "0.294"], ["Female", "313", "150", "163", ""], ["Tumor stage"], ["I ＋ II", "300", "168", "132", "0.002"], ["III ＋ IV", "249", "106", "143", ""], ["T stage"], ["T1 ＋ T2", "114", "76", "38", "<0.001*"], ["T3 ＋ T4", "452", "207", "245", ""], ["Lymph node status"], ["N0", "317", "176", "141", "0.004"], ["N1‐2", "247", "107", "140", ""], ["Metastasis"], ["M0", "419", "222", "197", "0.002"], ["M1", "80", "27", "53", ""], ["Residual tumor"], ["R0", "408", "218", "190", "0.030"], ["R1/2", "35", "12", "23", ""]], "row_count": 23, "column_count": 5, "numeric_cells": 53, "header_rows": 2, "locator": "section[17]/table-wrap[1]#cam41813-tbl-0002"}}, {"id": "asset:table:pmid:30714675:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:30617f8fe592ae9b2884cea024809cb9f837d8ed90fe6ba5d85b2f2457fe707c", "bytes": 637, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#cam41813-tbl-0001", "version": null, "note": "Overall information on the five prognostic lncRNAs", "structure": {"pmcid": "PMC6434209", "section_index": 15, "section_title": "Building a predictive model for prognosis and survival", "row_count": 7, "column_count": 6}, "table": {"label": "Table 1", "caption": "Overall information on the five prognostic lncRNAs", "rows": [["DElncRNAs", "Ensembl ID", "Univariate analysis", "Multivariate analysis"], ["HR", "P value", "HR", "P value"], ["H19", "ENSG00000130600", "1.098", "0.008**", "1.079", "0.038*"], ["MIR31HG", "ENSG00000171889", "0.821", "0.033*", "1.184", "0.025*"], ["HOTAIR", "ENSG00000228630", "1.111", "0.005**", "1.094", "0.019*"], ["WT1‐AS", "ENSG00000183242", "1.112", "0.034*", "1.103", "0.041*"], ["LINC00488", "ENSG00000214381", "0.754", "0.048*", "0.856", "0.106"]], "row_count": 7, "column_count": 6, "numeric_cells": 28, "header_rows": 2, "locator": "section[15]/table-wrap[1]#cam41813-tbl-0001"}}, {"id": "asset:table:pmid:30714675:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:80995975179e0e752896b2f681f7b5e00859f2bd8e59f91abe6164009633dfe7", "bytes": 874, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#cam41813-tbl-0002", "version": null, "note": "The correlations between the five‐lncRNA model and clinical features", "structure": {"pmcid": "PMC6434209", "section_index": 17, "section_title": "Combining risk score with clinical significance prognostic prediction for CRC", "row_count": 23, "column_count": 5}, "table": {"label": "Table 2", "caption": "The correlations between the five‐lncRNA model and clinical features", "rows": [["Variable", "Number", "Risk score"], ["Low risk", "High risk", "P value"], ["Age"], ["≤65", "251", "132", "119", "0.293"], ["＞65", "316", "151", "165", ""], ["Gender"], ["Male", "254", "133", "121", "0.294"], ["Female", "313", "150", "163", ""], ["Tumor stage"], ["I ＋ II", "300", "168", "132", "0.002"], ["III ＋ IV", "249", "106", "143", ""], ["T stage"], ["T1 ＋ T2", "114", "76", "38", "<0.001*"], ["T3 ＋ T4", "452", "207", "245", ""], ["Lymph node status"], ["N0", "317", "176", "141", "0.004"], ["N1‐2", "247", "107", "140", ""], ["Metastasis"], ["M0", "419", "222", "197", "0.002"], ["M1", "80", "27", "53", ""], ["Residual tumor"], ["R0", "408", "218", "190", "0.030"], ["R1/2", "35", "12", "23", ""]], "row_count": 23, "column_count": 5, "numeric_cells": 53, "header_rows": 2, "locator": "section[17]/table-wrap[1]#cam41813-tbl-0002"}}], "gaps": ["asset:data:geo:GSE38832 not downloaded", "asset:data:geo:GSE38832 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DERNA (DElncRNAs, DEmRNAs, and DEmiRNAs) data between tumor and normal samples were analyzed using “edgeR” package in R."}}, {"id": "method-2", "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"}}], "targets": [], "gaps": []}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "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": ["GSE38832"], "resolved_accessions": ["GSE38832"], "statements": ["The RNA‐Seq data and clinical information of CRC patients were completely downloaded from The Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/)."], "basis": "The paper names GSE38832 in Gene Expression Omnibus (GEO) Datasets of NCBI and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30714675", "data:geo:GSE38832", "asset:table:pmid:30714675:1", "asset:table:pmid:30714675:2", "asset:table:pmid:30714675:3", "asset:table:pmid:30714675:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE38832"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 24067, "completion_tokens": 1224, "cached_tokens": 784}}, "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:30714675", "type": "paper", "label": "pmid:30714675"}, {"id": "source:pmid:30714675", "type": "manuscript", "label": "PMID 30714675 full text"}, {"id": "data:geo:GSE38832", "type": "dataset", "label": "GEO GSE38832"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30714675", "type": "paper", "label": "pmid:30714675"}, {"id": "source:pmid:30714675", "type": "manuscript", "label": "PMID 30714675 full text"}, {"id": "data:geo:GSE38832", "type": "dataset", "label": "GEO GSE38832"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30714675", "type": "extraction", "used": ["source:pmid:30714675"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE38832", "type": "accession_resolution", "used": ["data:geo:GSE38832"], "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:30714675", "parent_hash": "sha256:290e4f2dbbc58b44bb99a358868cd6547e9351f869883965d42db04caba76c51", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE38832 licence not read", "asset:data:geo:GSE38832 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["their clinical potential as biomarkers. The RNA sequencing profiles of patients with colorectal cancer"], "order_basis": "paper_text_order:478", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DERNA (DElncRNAs, DEmRNAs, and DEmiRNAs) data between tumor and normal samples were analyzed using “edgeR” package in R."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}