Key genes in youth colorectal cancer based on data mining and verification by reverse transcription-quantitative PCR.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33574933", "kind": "science-record", "revision": 7, "content_hash": "sha256:d41c3f66504e19578e71f8ee25e0edc494be29ee8adbc1f7da527205d6b19754", "created_at": "2026-11-01T15:41:25Z", "updated_at": "2026-11-01T22:03:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Key genes in youth colorectal cancer based on data mining and verification by reverse transcription-quantitative PCR.", "doi": "10.3892/ol.2021.12455", "pmid": "33574933", "authors": ["Jianxin Chen", "Min Lin", "Yan Che", "Jian Guo", "Wei Lin"], "journal": "Oncology letters", "year": 2021, "abstract": "In recent years, among all patients with colorectal cancer, the proportion of young patients has been gradually increasing. However, the molecular mechanisms involved in colorectal cancer in the young are largely unknown. In the present study the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas datasets were integrated to elucidate the key gene biomarkers in these patients. The GSE41657 and GSE41258 datasets were downloaded from the GEO database. By screening for differentially expressed genes, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, protein-protein interaction analysis, hub gene screening and survival analysis, two key genes, CXCL8 and VEGFA, which were enriched in cancer pathways, were obtained. Reverse transcription-quantitative (RT-q)PCR was performed to verify the outcome obtained by bioinformatics analysis. In conclusion, the present study identified two key genes using bioinformatics analysis and RT-qPCR validation. These results indicated that the candidate genes may be involved in the progression of colorectal cancer in young people, and these two genes may act as ideal prognostic indicators or therapeutic targets for colorectal cancer in the youth.", "claims": [{"id": "claim-method", "statement": "GEO2R was used to identify the differentially expressed genes (DEGs) between youth colorectal cancer and normal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33574933", "locator": "sections[5] \"Data preprocessing and screening strategy\" paragraph 2", "quote": "GEO2R was used to identify the differentially expressed genes (DEGs) between youth colorectal cancer and normal tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used during the present study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33574933", "locator": "sections[22] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used during the present study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33574933"], "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:GSE41258"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE41258"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33574933", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2021.12455", "sha256": "sha256:3f4938ff80681a70d4d3d05af96c487e12b03e2c086b8f7dd954eb833475ce6e", "bytes": 20817, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ol.2021.12455", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7816307", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE41258", "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=GSE41258", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41258", "version": null, "note": "The datasets used during the present study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the present study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1012278", "GSM1012279", "GSM1012280", "GSM1012281", "GSM1012282", "GSM1012283", "GSM1012284", "GSM1012285", "GSM1012286", "GSM1012287", "GSM1012288", "GSM1012289", "GSM1012290", "GSM1012291", "GSM1012292", "GSM1012293", "GSM1012294", "GSM1012295", "GSM1012296", "GSM1012297", "GSM1012298", "GSM1012299", "GSM1012300", "GSM1012301", "GSM1012302", "GSM1012303", "GSM1012304", "GSM1012305", "GSM1012306", "GSM1012307", "GSM1012308", "GSM1012309", "GSM1012310", "GSM1012311", "GSM1012312", "GSM1012313", "GSM1012314", "GSM1012315", "GSM1012316", "GSM1012317", "GSM1012318", "GSM1012319", "GSM1012320", "GSM1012321", "GSM1012322", "GSM1012323", "GSM1012324", "GSM1012325", "GSM1012326", "GSM1012327", "GSM1012328", "GSM1012329", "GSM1012330", "GSM1012331", "GSM1012332", "GSM1012333", "GSM1012334", "GSM1012335", "GSM1012336", "GSM1012337", "GSM1012338", "GSM1012339", "GSM1012340", "GSM1012341", "GSM1012342", "GSM1012343", "GSM1012344", "GSM1012345", "GSM1012346", "GSM1012347", "GSM1012348", "GSM1012349", "GSM1012350", "GSM1012351", "GSM1012352", "GSM1012353", "GSM1012354", "GSM1012355", "GSM1012356", "GSM1012357", "GSM1012358", "GSM1012359", "GSM1012360", "GSM1012361", "GSM1012362", "GSM1012363", "GSM1012364", "GSM1012365", "GSM1012366", "GSM1012367", "GSM1012368", "GSM1012369", "GSM1012370", "GSM1012371", "GSM1012372", "GSM1012373", "GSM1012374", "GSM1012375", "GSM1012376", "GSM1012377", "GSM1012378", "GSM1012379", "GSM1012380", "GSM1012381", "GSM1012382", "GSM1012383", "GSM1012384", "GSM1012385", "GSM1012386", "GSM1012387", "GSM1012388", "GSM1012389", "GSM1012390", "GSM1012391", "GSM1012392", "GSM1012393", "GSM1012394", "GSM1012395", "GSM1012396", "GSM1012397", "GSM1012398", "GSM1012399", "GSM1012400", "GSM1012401", "GSM1012402", "GSM1012403", "GSM1012404", "GSM1012405", "GSM1012406", "GSM1012407", "GSM1012408", "GSM1012409", "GSM1012410", "GSM1012411", "GSM1012412", "GSM1012413", "GSM1012414", "GSM1012415", "GSM1012416", "GSM1012417", "GSM1012418", "GSM1012419", "GSM1012420", "GSM1012421", "GSM1012422", "GSM1012423", "GSM1012424", "GSM1012425", "GSM1012426", "GSM1012427", "GSM1012428", "GSM1012429", "GSM1012430", "GSM1012431", "GSM1012432", "GSM1012433", "GSM1012434", "GSM1012435", "GSM1012436", "GSM1012437", "GSM1012438", "GSM1012439", "GSM1012440", "GSM1012441", "GSM1012442", "GSM1012443", "GSM1012444", "GSM1012445", "GSM1012446", "GSM1012447", "GSM1012448", "GSM1012449", "GSM1012450", "GSM1012451", "GSM1012452", "GSM1012453", "GSM1012454", "GSM1012455", "GSM1012456", "GSM1012457", "GSM1012458", "GSM1012459", "GSM1012460", "GSM1012461", "GSM1012462", "GSM1012463", "GSM1012464", "GSM1012465", "GSM1012466", "GSM1012467", "GSM1012468", "GSM1012469", "GSM1012470", "GSM1012471", "GSM1012472", "GSM1012473", "GSM1012474", "GSM1012475", "GSM1012476", "GSM1012477", "GSM1012478", "GSM1012479", "GSM1012480", "GSM1012481", "GSM1012482", "GSM1012483", "GSM1012484", "GSM1012485", "GSM1012486", "GSM1012487", "GSM1012488", "GSM1012489", "GSM1012490", "GSM1012491", "GSM1012492", "GSM1012493", "GSM1012494", "GSM1012495", "GSM1012496", "GSM1012497", "GSM1012498", "GSM1012499", "GSM1012500", "GSM1012501", "GSM1012502", "GSM1012503", "GSM1012504", "GSM1012505", "GSM1012506", "GSM1012507", "GSM1012508", "GSM1012509", "GSM1012510", "GSM1012511", "GSM1012512", "GSM1012513", "GSM1012514", "GSM1012515", "GSM1012516", "GSM1012517", "GSM1012518", "GSM1012519", "GSM1012520", "GSM1012521", "GSM1012522", "GSM1012523", "GSM1012524", "GSM1012525", "GSM1012526", "GSM1012527", "GSM1012528", "GSM1012529", "GSM1012530", "GSM1012531", "GSM1012532", "GSM1012533", "GSM1012534", "GSM1012535", "GSM1012536", "GSM1012537", "GSM1012538", "GSM1012539", "GSM1012540", "GSM1012541", "GSM1012542", "GSM1012543", "GSM1012544", "GSM1012545", "GSM1012546", "GSM1012547", "GSM1012548", "GSM1012549", "GSM1012550", "GSM1012551", "GSM1012552", "GSM1012553", "GSM1012554", "GSM1012555", "GSM1012556", "GSM1012557", "GSM1012558", "GSM1012559", "GSM1012560", "GSM1012561", "GSM1012562", "GSM1012563", "GSM1012564", "GSM1012565", "GSM1012566", "GSM1012567", "GSM1012568", "GSM1012569", "GSM1012570", "GSM1012571", "GSM1012572", "GSM1012573", "GSM1012574", "GSM1012575", "GSM1012576", "GSM1012577", "GSM1012578", "GSM1012579", "GSM1012580", "GSM1012581", "GSM1012582", "GSM1012583", "GSM1012584", "GSM1012585", "GSM1012586", "GSM1012587", "GSM1012588", "GSM1012589", "GSM1012590", "GSM1012591", "GSM1012592", "GSM1012593", "GSM1012594", "GSM1012595", "GSM1012596", "GSM1012597", "GSM1012598", "GSM1012599", "GSM1012600", "GSM1012601", "GSM1012602", "GSM1012603", "GSM1012604", "GSM1012605", "GSM1012606", "GSM1012607", "GSM1012608", "GSM1012609", "GSM1012610", "GSM1012611", "GSM1012612", "GSM1012613", "GSM1012614", "GSM1012615", "GSM1012616", "GSM1012617", "GSM1012618", "GSM1012619", "GSM1012620", "GSM1012621", "GSM1012622", "GSM1012623", "GSM1012624", "GSM1012625", "GSM1012626", "GSM1012627", "GSM1012628", "GSM1012629", "GSM1012630", "GSM1012631", "GSM1012632", "GSM1012633", "GSM1012634", "GSM1012635", "GSM1012636", "GSM1012637", "GSM1012638", "GSM1012639", "GSM1012640", "GSM1012641", "GSM1012642", "GSM1012643", "GSM1012644", "GSM1012645", "GSM1012646", "GSM1012647", "GSM1012648", "GSM1012649", "GSM1012650", "GSM1012651", "GSM1012652", "GSM1012653", "GSM1012654", "GSM1012655", "GSM1012656", "GSM1012657", "GSM1012658", "GSM1012659", "GSM1012660", "GSM1012661", "GSM1012662", "GSM1012663", "GSM1012664", "GSM1012665", "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}}, {"id": "data:geo:GSE41657", "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=GSE41657", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41657", "version": null, "note": "The datasets used during the present study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the present study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1021121", "GSM1021122", "GSM1021123", "GSM1021124", "GSM1021125", "GSM1021126", "GSM1021127", "GSM1021128", "GSM1021129", "GSM1021130", "GSM1021131", "GSM1021132", "GSM1021133", "GSM1021134", "GSM1021135", "GSM1021136", "GSM1021137", "GSM1021138", "GSM1021139", "GSM1021140", "GSM1021141", "GSM1021142", "GSM1021143", "GSM1021144", "GSM1021145", "GSM1021146", "GSM1021147", "GSM1021148", "GSM1021149", "GSM1021150", "GSM1021151", "GSM1021152", "GSM1021153", "GSM1021154", "GSM1021155", "GSM1021156", "GSM1021157", "GSM1021158", "GSM1021159", "GSM1021160", "GSM1021161", "GSM1021162", "GSM1021163", "GSM1021164", "GSM1021165", "GSM1021166", "GSM1021167", "GSM1021168", "GSM1021169", "GSM1021170", "GSM1021171", "GSM1021172", "GSM1021173", "GSM1021174", "GSM1021175", "GSM1021176", "GSM1021177", "GSM1021178", "GSM1021179", "GSM1021180", "GSM1021181", "GSM1021182", "GSM1021183", "GSM1021184", "GSM1021185", "GSM1021186", "GSM1021187", "GSM1021188", "GSM1021189", "GSM1021190", "GSM1021191", "GSM1021192", "GSM1021193", "GSM1021194", "GSM1021195", "GSM1021196", "GSM1021197", "GSM1021198", "GSM1021199", "GSM1021200", "GSM1021201", "GSM1021202", "GSM1021203", "GSM1021204", "GSM1021205", "GSM1021206", "GSM1021207", "GSM1021208"], "sample_count": 88, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Gene expression profiling of colorectal normal mucosa, adenoma and adenocarcinoma tissues", "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:GSE41258 not downloaded", "asset:data:geo:GSE41258 licence not read", "asset:data:geo:GSE41657 not downloaded", "asset:data:geo:GSE41657 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"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": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R was used to identify the differentially expressed genes (DEGs) between youth colorectal cancer and normal tissues."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE41657", "GSE41258"], "resolved_accessions": ["GSE41657", "GSE41258"], "statements": ["The datasets used during the present study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE41657, GSE41258 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33574933", "data:geo:GSE41258"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE41258"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 15833, "completion_tokens": 1630, "cached_tokens": 792}}, "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:33574933", "type": "paper", "label": "pmid:33574933"}, {"id": "source:pmid:33574933", "type": "manuscript", "label": "PMID 33574933 full text"}, {"id": "data:geo:GSE41258", "type": "dataset", "label": "GEO GSE41258"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33574933", "type": "paper", "label": "pmid:33574933"}, {"id": "source:pmid:33574933", "type": "manuscript", "label": "PMID 33574933 full text"}, {"id": "data:geo:GSE41258", "type": "dataset", "label": "GEO GSE41258"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33574933", "type": "extraction", "used": ["source:pmid:33574933"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE41258", "type": "accession_resolution", "used": ["data:geo:GSE41258"], "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:33574933", "parent_hash": "sha256:f6fa1575fa375efb22331bdf8eca957b23a4406a8701ec2425a4fdd78013a3bb", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE41258 licence not read", "asset:data:geo:GSE41258 not downloaded", "asset:data:geo:GSE41657 licence not read", "asset:data:geo:GSE41657 not downloaded", "execution.not_run", "method.reader_named_unmapped", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["key genes using bioinformatics analysis and RT-qPCR validation. These results indicated that the", "y genes using bioinformatics analysis and RT-qPCR validation. These results indicated that the"], "order_basis": "paper_text_order:1042", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Student's t-test"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}