Identification of genomic expression differences between right-sided and left-sided colon cancer based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29430186", "kind": "science-record", "revision": 9, "content_hash": "sha256:42a4650fba55d714a120d2fb85641445569d0848990e07df73c53b37f599ef60", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T22:43:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of genomic expression differences between right-sided and left-sided colon cancer based on bioinformatics analysis.", "doi": "10.2147/OTT.S154207", "pmid": "29430186", "authors": ["Qiliang Peng", "Kaisu Lin", "Tao Chang", "Li Zou", "Pengfei Xing", "Yuntian Shen", "Yaqun Zhu"], "journal": "OncoTargets and therapy", "year": 2018, "abstract": "INTRODUCTION: More and more findings have demonstrated that right-sided colon cancers (RCC) and left-sided colon cancers (LCC) are distinct clinical and biological entities and suggest that they should be treated as different diseases. However, the reasons why RCC and LCC harbor different clinical and biological features remain unclear.\nMATERIALS AND METHODS: To identify the genomic expression differences between RCC and LCC and uncover the mechanisms underlying these differences, we chose the gene expression profiles of GSE14333 from the Gene Expression Omnibus (GEO) database as an object of study. Then, a systematic and integrative bioinformatics analysis was performed to research the possible mechanism of the differentially expressed (DE) genes from the Gene Expression Omnibus dataset including gene ontology (GO) analysis, pathway enrichment analysis, protein-protein interaction (PPI) network construction, and module analysis. Totally, we extracted 3,793 DE genes from samples of colon cancer including 1,961 genes upregulated in RCC and 1,832 genes upregulated in LCC from the selected dataset.\nRESULTS: The results of GO and pathway enrichment analysis indicated that RCC and LCC could predispose to different pathways regulated by different genes. Based on the PPI network, PCNA, TP53, HSP90AA1, CSNK2A1, UBB, LRRK2, ABL1, PRKACA, CAV1, and JUN were identified as the key hub genes. Also, significant modules were screened from the PPI network.\nCONCLUSION: In conclusion, the present study indicated that the identified genes and pathways may promote new insights into the underlying molecular mechanisms contributing to the difference between RCC and LCC and might be used as specific therapeutic targets and prognostic markers for the personalized treatment of RCC and LCC.", "claims": [{"id": "claim-method", "statement": "The differential expression analysis was carried out on the basis of Student’s t-test in the Limma R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29430186", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "The differential expression analysis was carried out on the basis of Student’s t-test in the Limma R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data (GSE14333) were retrieved from the public database National Center for Biotechnology Information Gene Expression Omnibus. GSE14333 was based on the GPL570 platform, which is determined by Affymetrix Human Genome U133Plus 2.0 arrays. We only evaluated the genome expression data with clinical data of the patients provided by the submitter. Finally, we selected the data consist of 101 RCC patients and 93 LCC patients, which were part of GSE14333. Normalized gene expression data were downloaded as the direct form for further analysis, and the dataset contained the expression information of 23,495 mRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29430186", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The microarray data (GSE14333) were retrieved from the public database National Center for Biotechnology Information Gene Expression Omnibus."}, {"asset": "source:pmid:29430186", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "GSE14333 was based on the GPL570 platform, which is determined by Affymetrix Human Genome U133Plus 2.0 arrays."}, {"asset": "source:pmid:29430186", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "We only evaluated the genome expression data with clinical data of the patients provided by the submitter."}, {"asset": "source:pmid:29430186", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "Finally, we selected the data consist of 101 RCC patients and 93 LCC patients, which were part of GSE14333."}, {"asset": "source:pmid:29430186", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "Normalized gene expression data were downloaded as the direct form for further analysis, and the dataset contained the expression information of 23,495 mRNAs."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GSE14333 gene-expression profiles retrieved from GEO and analyzed with the Limma R package at P-value <0.05, the study identified 3,793 differentially expressed genes between right-sided and left-sided colon cancers.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Based on the Limma R package, a total of 3,793 genes were identified to differentially express between RCC and LCC patients (P-value <0.05), of which 1,961 genes were upregulated and 1,832 genes were downregulated in RCC compared with LCC."}, "evidence": [{"asset": "source:pmid:29430186", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "To identify the genomic expression differences between RCC and LCC and uncover the mechanisms underlying these differences, we chose the gene expression profiles of GSE14333 from the Gene Expression Omnibus (GEO) database as an object of study."}, {"asset": "source:pmid:29430186", "locator": "sections[9] \"Identification of DE genes\" paragraph 2", "quote": "Based on the Limma R package, a total of 3,793 genes were identified to differentially express between RCC and LCC patients (P-value <0.05), of which 1,961 genes were upregulated and 1,832 genes were downregulated in RCC compared with LCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GSE14333 gene-expression profiles retrieved from GEO and analyzed with the Limma R package at P-value <0.05, the study identified 3,793 differentially expressed genes between right-sided and left-sided colon cancers.", "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:29430186"], "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:GSE14333"], "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:GSE14333"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29430186", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S154207", "sha256": "sha256:715c32a9739c20f5369fe1d1c8bf0674965416514cf43d29c8c6a44343247a3a", "bytes": 31490, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S154207", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5797455", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14333", "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=GSE14333", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14333", "version": null, "note": "The microarray data (GSE14333) were retrieved from the public database National Center for Biotechnology Information Gene Expression Omnibus. GSE14333 was based on the GPL570 platform, which is determined by Affymetrix Human Genome U133Plus 2.0 arrays. We only evaluated the genome expression data with clinical data of the patients provided by the submitter. Finally, we selected the data consist of 101 RCC patients and 93 LCC patients, which were part of GSE14333. Normalized gene expression data were downloaded as the direct form for further analysis, and the dataset contained the expression information of 23,495 mRNAs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data (GSE14333) were retrieved from the public database National Center for Biotechnology Information Gene Expression Omnibus. GSE14333 was based on the GPL570 platform, which is determined by Affymetrix Human Genome U133Plus 2.0 arrays. We only evaluated the genome expression data with clinical data of the patients provided by the submitter. Finally, we selected the data consist of 101 RCC patients and 93 LCC patients, which were part of GSE14333. Normalized gene expression data were downloaded as the direct form for further analysis, and the dataset contained the expression information of 23,495 mRNAs.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM358341", "GSM358342", "GSM358343", "GSM358344", "GSM358345", "GSM358346", "GSM358347", "GSM358348", "GSM358349", "GSM358350", "GSM358351", "GSM358352", "GSM358353", "GSM358354", "GSM358355", "GSM358356", "GSM358357", "GSM358358", "GSM358359", "GSM358360", "GSM358361", "GSM358362", "GSM358363", "GSM358364", "GSM358365", "GSM358366", "GSM358367", "GSM358368", "GSM358369", "GSM358370", "GSM358371", "GSM358372", "GSM358373", "GSM358374", "GSM358375", "GSM358376", "GSM358377", "GSM358378", "GSM358379", "GSM358380", "GSM358381", "GSM358382", "GSM358383", "GSM358384", "GSM358385", "GSM358386", "GSM358387", "GSM358388", "GSM358389", "GSM358390", "GSM358391", "GSM358392", "GSM358393", "GSM358394", "GSM358395", "GSM358396", "GSM358397", "GSM358398", "GSM358399", "GSM358400", "GSM358401", "GSM358402", "GSM358403", "GSM358404", "GSM358405", "GSM358406", "GSM358407", "GSM358408", "GSM358409", "GSM358410", "GSM358411", "GSM358412", "GSM358413", "GSM358414", "GSM358415", "GSM358416", "GSM358417", "GSM358418", "GSM358419", "GSM358420", "GSM358421", "GSM358422", "GSM358423", "GSM358424", "GSM358425", "GSM358426", "GSM358427", "GSM358428", "GSM358429", "GSM358430", "GSM358431", "GSM358432", "GSM358433", "GSM358434", "GSM358435", "GSM358436", "GSM358437", "GSM358438", "GSM358439", "GSM358440", "GSM358441", "GSM358442", "GSM358443", "GSM358444", "GSM358445", "GSM358446", "GSM358447", "GSM358448", "GSM358449", "GSM358450", "GSM358451", "GSM358452", "GSM358453", "GSM358454", "GSM358455", "GSM358456", "GSM358457", "GSM358458", "GSM358459", "GSM358460", "GSM358461", "GSM358462", "GSM358463", "GSM358464", "GSM358465", "GSM358466", "GSM358467", "GSM358468", "GSM358469", "GSM358470", "GSM358471", "GSM358472", "GSM358473", "GSM358474", "GSM358475", "GSM358476", "GSM358477", "GSM358478", "GSM358479", "GSM358480", "GSM358481", "GSM358482", "GSM358483", "GSM358484", "GSM358485", "GSM358486", "GSM358487", "GSM358488", "GSM358489", "GSM358490", "GSM358491", "GSM358492", "GSM358493", "GSM358494", "GSM358495", "GSM358496", "GSM358497", "GSM358498", "GSM358499", "GSM358500", "GSM358501", "GSM358502", "GSM358503", "GSM358504", "GSM358505", "GSM358506", "GSM358507", "GSM358508", "GSM358509", "GSM358510", "GSM358511", "GSM358512", "GSM358513", "GSM358514", "GSM358515", "GSM358516", "GSM358517", "GSM358518", "GSM358519", "GSM358520", "GSM358521", "GSM358522", "GSM358523", "GSM358524", "GSM358525", "GSM358526", "GSM358527", "GSM358528", "GSM358529", "GSM358530", "GSM358531", "GSM358532", "GSM358533", "GSM358534", "GSM358535", "GSM358536", "GSM358537", "GSM358538", "GSM358539", "GSM358540", "GSM358541", "GSM358542", "GSM358543", "GSM358544", "GSM358545", "GSM358546", "GSM358547", "GSM358548", "GSM358549", "GSM358550", "GSM358551", "GSM358552", "GSM358553", "GSM358554", "GSM358555", "GSM358556", "GSM358557", "GSM358558", "GSM358559", "GSM358560", "GSM358561", "GSM358562", "GSM358563", "GSM358564", "GSM358565", "GSM358566", "GSM358567", "GSM358568", "GSM358569", "GSM358570", "GSM358571", "GSM358572", "GSM358573", "GSM358574", "GSM358575", "GSM358576", "GSM358577", "GSM358578", "GSM358579", "GSM358580", "GSM358581", "GSM358582", "GSM358583", "GSM358584", "GSM358585", "GSM358586", "GSM358587", "GSM358588", "GSM358589", "GSM358590", "GSM358591", "GSM358592", "GSM358593", "GSM358594", "GSM358595", "GSM358596", "GSM358597", "GSM358598", "GSM358599", "GSM358600", "GSM358601", "GSM358602", "GSM358603", "GSM358604", "GSM358605", "GSM358606", "GSM358607", "GSM358608", "GSM358609", "GSM358610", "GSM358611", "GSM358612", "GSM358613", "GSM358614", "GSM358615", "GSM358616", "GSM358617", "GSM358618", "GSM358619", "GSM358620", "GSM358621", "GSM358622", "GSM358623", "GSM358624", "GSM358625", "GSM358626", "GSM358627", "GSM358628", "GSM358629", "GSM358630"], "sample_count": 290, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from 290 primary colorectal cancers", "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:29430186:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b137afc3fcc625c08d30b1c8b82d596838b39e20dd83a079e418b6d299998392", "bytes": 569, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#t1-ott-11-609", "version": null, "note": "Clinical characteristics of the study population with RCC and LCC", "structure": {"pmcid": "PMC5797455", "section_index": 8, "section_title": "Patient characteristics", "row_count": 11, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinical characteristics of the study population with RCC and LCC", "rows": [["Clinical characteristics", "RCC", "LCC"], ["Patients", "101", "93"], ["Median age (years)", "69±12", "62±13"], ["Sex", "", ""], ["Male", "46 (45.5%)", "55 (59.1%)"], ["Female", "55 (54.5%)", "38 (40.9%)"], ["Dukes staging system", "", ""], ["A", "16 (15.8%)", "16 (17.2%)"], ["B", "44 (43.6%)", "37 (39.8%)"], ["C", "41 (40.6%)", "40 (43.0%)"], ["DFS", "41±27", "44±28"]], "row_count": 11, "column_count": 3, "numeric_cells": 16, "header_rows": 1, "locator": "section[8]/table-wrap[1]#t1-ott-11-609"}}, {"id": "asset:table:pmid:29430186:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f97d437a9f2c72e8c0ce2bc386eb9790313e9c52ad7cafba7dfdc48bd52cad44", "bytes": 2481, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#t2-ott-11-609", "version": null, "note": "Top 50 upregulated DE genes in RCC and LCC", "structure": {"pmcid": "PMC5797455", "section_index": 9, "section_title": "Identification of DE genes", "row_count": 27, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top 50 upregulated DE genes in RCC and LCC", "rows": [["RCC", "LCC"], ["Gene", "P-value", "Gene", "P-value", "Gene", "P-value", "Gene", "P-value"], ["HOXC6", "7.35E–10", "TIGD2", "5.88E–05", "PRAC1", "2.32E–26", "FXYD1", "1.36E–05"], ["GLOD4", "2.11E–07", "ME2", "6.86E–05", "HOXB13", "6.94E–08", "CPE", "1.40E–05"], ["FLRT3", "2.50E–07", "AHR", "7.53E–05", "AX748273", "1.15E–07", "DBNDD2", "1.50E–05"], ["PAX9", "3.64E–07", "MSX2", "8.17E–05", "MUC12", "3.09E–07", "ZNF813", "1.50E–05"], ["CDC42EP2", "6.88E–07", "PSMC4", "8.80E–05", "LY6G6D", "5.53E–07", "ZNF347", "2.19E–05"], ["TC2N", "1.04E–06", "BSG", "8.84E–05", "ZNF610", "7.34E–07", "STMN2", "2.19E–05"], ["ZIC2", "1.28E–06", "AX747191", "9.21E–05", "ST6GAL2", "1.51E–06", "GNG4", "2.36E–05"], ["FOXD1", "2.17E–06", "ALAS1", "9.58E–05", "KHDRBS3", "2.07E–06", "TMSB15A", "2.42E–05"], ["NDUFV2", "1.98E–05", "CAMK2D", "9.60E–05", "AKAP2", "2.49E–06", "MIR6716", "2.59E–05"], ["VPS53", "1.99E–05", "DDIT3", "9.61E–05", "FGD1", "2.50E–06", "SLC22A17", "2.68E–05"], ["AARS2", "2.01E–05", "PIK3R3", "9.89E–05", "ELAVL2", "2.70E–06", "DDX27", "2.77E–05"], ["ESCO1", "2.18E–05", "RP11-61L19.3", "1.00E–05", "INSL5", "2.88E–06", "IFNLR1", "2.97E–05"], ["DEGS2", "2.23E–05", "IRF9", "1.19E–04", "XPNPEP2", "3.32E–06", "SERINC3", "3.04E–05"], ["SNRPD1", "2.28E–05", "PRMT5", "1.23E–04", "MAGEH1", "3.52E–06", "SLC35D3", "3.22E–05"], ["KIAA1468", "2.73E–05", "GMDS", "1.25E–04", "DPM1", "3.55E–06", "GPR153", "3.28E–05"], ["RBBP8", "2.83E–05", "ZIC5", "1.37E–04", "TLE2", "3.78E–06", "ZNF134", "3.32E–05"], ["OR6A2", "2.96E–05", "GOT1", "1.37E–04", "OGN", "4.83E–06", "PLAGL2", "3.34E–05"], ["ABCB11", "3.31E–05", "FAM46A", "1.40E–04", "ZNF415", "5.73E–06", "CLDN8", "3.48E–05"], ["GAPDH", "3.42E–05", "SLC10A2", "1.49E–04", "WASF3", "6.02E–06", "KLHL34", "3.57E–05"], ["EIF4A1", "4.01E–05", "DAOA", "1.60E–04", "BCAS4", "6.85E–06", "NES", "3.65E–05"], ["HOXB6", "4.16E–05", "MOK", "1.66E–04", "CERK", "7.11E–06", "ROCK2", "3.73E–05"], ["EIF2B2", "4.68E–05", "SEMG1", "1.73E–04", "CHMP4B", "7.88E–06", "KLF7", "4.12E–05"], ["DGKQ", "4.84E–05", "HSPA4L", "1.82E–04", "ZFP28", "9.09E–06", "ZCCHC24", "4.73E–05"], ["DNAH2", "5.34E–05", "GCH1", "1.83E–04", "ZNF542P", "1.25E–05", "RP11-524D16_A.3", "4.95E–05"], ["SDHA", "5.35E–05", "TIMM50", "1.89E–04", "PDE3A", "1.25E–05", "SPIN3", "5.22E–05"]], "row_count": 27, "column_count": 8, "numeric_cells": 128, "header_rows": 2, "locator": "section[9]/table-wrap[1]#t2-ott-11-609"}}, {"id": "asset:table:pmid:29430186:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a15e5b002bb2298e33311c254fecf64a875fbdc90d770fd159b144c4d5c3455", "bytes": 472, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t3-ott-11-609", "version": null, "note": "Topological information of networks detected by the upregulated genes in RCC and LCC, respectively", "structure": {"pmcid": "PMC5797455", "section_index": 12, "section_title": "PPI network construction", "row_count": 3, "column_count": 5}, "table": {"label": "Table 3", "caption": "Topological information of networks detected by the upregulated genes in RCC and LCC, respectively", "rows": [["Network", "Number of nodes", "Number of edges", "Average number of neighbors", "Hub genes"], ["RCC", "804", "1,759", "4.38", "UBB, HSP90AA1, TP53, PCNA, CSNK2A1"], ["LCC", "589", "872", "2.96", "PRKACA, CAV1, LRRK2, ABL1, JUN"]], "row_count": 3, "column_count": 5, "numeric_cells": 7, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t3-ott-11-609"}}, {"id": "asset:table:pmid:29430186:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a195ab1ee44b8476decac01d1d87a385fe425b7151bc70567ab693c774b99d8f", "bytes": 553, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#t4-ott-11-609", "version": null, "note": "Detailed information of the selected hub genes from the PPI network", "structure": {"pmcid": "PMC5797455", "section_index": 12, "section_title": "PPI network construction", "row_count": 11, "column_count": 4}, "table": {"label": "Table 4", "caption": "Detailed information of the selected hub genes from the PPI network", "rows": [["Gene", "Network", "P-value", "Degree"], ["UBB", "RCC", "0.012", "81"], ["HSP90AA1", "RCC", "0.012", "75"], ["TP53", "RCC", "0.003", "71"], ["PCNA", "RCC", "0.005", "35"], ["CSNK2A1", "RCC", "0.002", "33"], ["PRKACA", "LCC", "0.049", "26"], ["CAV1", "LCC", "0.007", "25"], ["LRRK2", "LCC", "0.021", "18"], ["ABL1", "LCC", "0.002", "18"], ["JUN", "LCC", "0.010", "18"]], "row_count": 11, "column_count": 4, "numeric_cells": 22, "header_rows": 1, "locator": "section[12]/table-wrap[2]#t4-ott-11-609"}}], "gaps": ["asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE14333 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "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 differential expression analysis was carried out on the basis of Student’s t-test in the Limma R package."}}, {"id": "method-2", "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-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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: limma_voom."}, "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": ["GSE14333"], "resolved_accessions": ["GSE14333"], "statements": ["The microarray data (GSE14333) were retrieved from the public database National Center for Biotechnology Information Gene Expression Omnibus. GSE14333 was based on the GPL570 platform, which is determined by Affymetrix Human Genome U133Plus 2.0 arrays. We only evaluated the genome expression data with clinical data of the patients provided by the submitter. Finally, we selected the data consist of 101 RCC patients and 93 LCC patients, which were part of GSE14333. Normalized gene expression data were downloaded as the direct form for further analysis, and the dataset contained the expression information of 23,495 mRNAs."], "basis": "The paper names GSE14333 in National Center for Biotechnology Information Gene Expression Omnibus (GEO) 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:29430186", "data:geo:GSE14333", "asset:table:pmid:29430186:1", "asset:table:pmid:29430186:2", "asset:table:pmid:29430186:3", "asset:table:pmid:29430186:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14333"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:41Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 64567, "completion_tokens": 3077, "cached_tokens": 2105}}, "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:29430186", "type": "paper", "label": "pmid:29430186"}, {"id": "source:pmid:29430186", "type": "manuscript", "label": "PMID 29430186 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29430186", "type": "paper", "label": "pmid:29430186"}, {"id": "source:pmid:29430186", "type": "manuscript", "label": "PMID 29430186 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29430186", "type": "extraction", "used": ["source:pmid:29430186"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14333", "type": "accession_resolution", "used": ["data:geo:GSE14333"], "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:29430186", "parent_hash": "sha256:8a86463fa496874cbffd7014718109cdd1bc1012ae26670edf638771825a0d7c", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE14333 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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 differential expression analysis was carried out on the basis of Student’s t-test in the Limma R package."], "order_basis": "analysis_only", "id": "assay:1"}]}