Update of gene expression/methylation and MiRNA profiling in colorectal cancer; application in diagnosis, prognosis, and targeted therapy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35333898", "kind": "science-record", "revision": 4, "content_hash": "sha256:52f28689a11725eaab21ecf90a298f7fcce0178d41bd75854e92aab2e788252d", "created_at": "2026-11-01T18:14:08Z", "updated_at": "2026-11-01T22:06:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Update of gene expression/methylation and MiRNA profiling in colorectal cancer; application in diagnosis, prognosis, and targeted therapy.", "doi": "10.1371/journal.pone.0265527", "pmid": "35333898", "authors": ["Amir Mehrgou", "Shahram Teimourian"], "journal": "PloS one", "year": 2022, "abstract": "BACKGROUND: Colorectal cancer is one of the most deadliest malignancies worldwide. Due to the dearth of appropriate biomarkers, the diagnosis of this mortal disease is usually deferred, in its turn, culminating in the failure of prevention. By the same token, proper biomarkers are at play in determining the quality of prognosis. In other words, the survival rate is contingent upon the regulation of such biomarkers.\nMATERIALS AND METHODS: The information regarding expression (GSE41258, and GSE31905), methylation (GSE101764), and miRNA (dbDEMC) were downloaded. MEXPRESS and GEPIA confirmed the validated differentially expressed/methylated genes using TCGA data. Taking advantage of the correlation plots and receiver-operating-characteristic (ROC) curves, expression and methylation profiles were compared. The interactions between validated differentially expressed genes and differentially expressed miRNA were recognized and visualized by miRTarBase and Cytoscape, respectively. Then, the protein-protein interaction (PPI) network and hub genes were established via STRING and Cytohubba plugin. Utilizing R packages (DOSE, Enrichplot, and clusterProfiler) and DAVID database, the Functional Enrichment analysis and the detection of KEGG pathways were performed. Ultimately, in order to recognize the prognostic value of found biomarkers, they were evaluated through drawing survival plots for CRC patients.\nRESULTS: In this research, we found an expression profile (with 13 novel genes), a methylation profile (with two novel genes), and a miRNA profile with diagnostic value. Concerning diagnosis, the expression profile was evaluated more powerful in comparison with the methylation profile. Furthermore, a prognosis-related expression profile was detected.\nCONCLUSION: In addition to diagnostic- and prognostic-applicability, the discerned profiles can assist in targeted therapy and current therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "Utilizing GEO2R, an online differentially analyzing tool, and “GEOquery” (Version 2.54.0) [66], and “Limma” (Version 3.42.0) [67] R (Version 3.6.3) packages, we exerted log2 transformation and Benjamini & Hochberg method on GSE41258 to find the differentially expressed genes in a case/control comparison manner.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35333898", "locator": "sections[17] \"5.2. Identification of Differentially Expressed Genes (DEGs) and Differentially Methylated Genes (DMGs)\" paragraph 2", "quote": "Utilizing GEO2R, an online differentially analyzing tool, and “GEOquery” (Version 2.54.0) [66], and “Limma” (Version 3.42.0) [67] R (Version 3.6.3) packages, we exerted log2 transformation and Benjamini & Hochberg method on GSE41258 to find the differentially expressed genes in a case/control comparison manner."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41258 (GSE41258), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101764 (GSE101764), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31905 (GSE31905)].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35333898", "locator": "sections[30] \"Data Availability\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41258 (GSE41258), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101764 (GSE101764), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31905 (GSE31905)]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In this research, we found an expression profile (with 13 novel genes), a methylation profile (with two novel genes), and a miRNA profile with diagnostic value.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35333898", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In this research, we found an expression profile (with 13 novel genes), a methylation profile (with two novel genes), and a miRNA profile with diagnostic value."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In this research, we found an expression profile (with 13 novel genes), a methylation profile (with two novel genes), and a miRNA profile with diagnostic value.", "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:35333898"], "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:GSE101764"], "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:GSE101764"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35333898", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0265527", "sha256": 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"GSM1012666", "GSM1012667"], "sample_count": 390, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from colorectal cancer patients", "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:GSE101764 not downloaded", "asset:data:geo:GSE101764 licence not read", "asset:data:geo:GSE31905 not downloaded", "asset:data:geo:GSE31905 licence not read", "asset:data:geo:GSE41258 not downloaded", "asset:data:geo:GSE41258 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": 0.8, "band": "high", "quote": 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"band": "verbatim", "quote": "Utilizing GEO2R, an online differentially analyzing tool, and “GEOquery” (Version 2.54.0) [66], and “Limma” (Version 3.42.0) [67] R (Version 3.6.3) packages, we exerted log2 transformation and Benjamini & Hochberg method on GSE41258 to find the differentially expressed genes in a case/control comparison manner."}}], "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": ["GSE41258", "GSE101764", "GSE31905"], "resolved_accessions": ["GSE41258", "GSE101764", "GSE31905"], "statements": ["The datasets supporting the conclusions of this article are available in the Gene Expression Omnibus repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41258 (GSE41258), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101764 (GSE101764), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31905 (GSE31905)]."], "basis": "The paper names GSE41258, GSE101764, GSE31905 in Gene Expression Omnibus repository 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:35333898", "data:geo:GSE101764"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE101764"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:39:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 19694, "completion_tokens": 2019, "cached_tokens": 128}}, "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:35333898", "type": "paper", "label": "pmid:35333898"}, {"id": "source:pmid:35333898", "type": "manuscript", "label": "PMID 35333898 full text"}, {"id": "data:geo:GSE101764", "type": "dataset", "label": "GEO GSE101764"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35333898", "type": "paper", "label": "pmid:35333898"}, {"id": "source:pmid:35333898", "type": "manuscript", "label": "PMID 35333898 full text"}, {"id": "data:geo:GSE101764", "type": "dataset", "label": "GEO GSE101764"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35333898", "type": "extraction", "used": ["source:pmid:35333898"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE101764", "type": "accession_resolution", "used": ["data:geo:GSE101764"], "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:35333898", "parent_hash": "sha256:763766db01099420bceb7f8a2d2f5bfca5ed3ab9f79ba1d4aa3a3a69dff6b5f7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE101764 licence not read", "asset:data:geo:GSE101764 not downloaded", "asset:data:geo:GSE31905 licence not read", "asset:data:geo:GSE31905 not downloaded", "asset:data:geo:GSE41258 licence not read", "asset:data:geo:GSE41258 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": 0.8, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}