Screening of gene markers related to the prognosis of metastatic skin cutaneous melanoma based on Logit regression and survival analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33823876", "kind": "science-record", "revision": 7, "content_hash": "sha256:71e9fcc819e743b850482a4e42bd54dd9985280d53e70b970073a94e89d497c3", "created_at": "2026-11-01T15:41:31Z", "updated_at": "2026-11-01T22:03:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of gene markers related to the prognosis of metastatic skin cutaneous melanoma based on Logit regression and survival analysis.", "doi": "10.1186/s12920-021-00923-0", "pmid": "33823876", "authors": ["Guoliang Jia", "Zheyu Song", "Zhonghang Xu", "Youmao Tao", "Yuanyu Wu", "Xiaoyu Wan"], "journal": "BMC medical genomics", "year": 2021, "abstract": "BACKGROUND: Bioinformatics was used to analyze the skin cutaneous melanoma (SKCM) gene expression profile to provide a theoretical basis for further studying the mechanism underlying metastatic SKCM and the clinical prognosis.\nMETHODS: We downloaded the gene expression profiles of 358 metastatic and 102 primary (nonmetastatic) CM samples from The Cancer Genome Atlas (TCGA) database as a training dataset and the GSE65904 dataset from the National Center for Biotechnology Information database as a validation dataset. Differentially expressed genes (DEGs) were screened using the limma package of R3.4.1, and prognosis-related feature DEGs were screened using Logit regression (LR) and survival analyses. We also used the STRING online database, Cytoscape software, and Database for Annotation, Visualization and Integrated Discovery software for protein-protein interaction network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses based on the screened DEGs.\nRESULTS: Of the 876 DEGs selected, 11 (ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C) were screened using LR analysis. The survival prognosis of nonmetastatic group was better compared to the metastatic group between the TCGA training and validation datasets. The 11 DEGs were involved in 9 KEGG signaling pathways, and of these 11 DEGs, CALML5 was a feature DEG involved in the melanogenesis pathway, 12 targets of which were collected.\nCONCLUSION: The feature DEGs screened, such as CALML5, are related to the prognosis of metastatic CM according to LR. Our results provide new ideas for exploring the molecular mechanism underlying CM metastasis and finding new diagnostic prognostic markers.", "claims": [{"id": "claim-method", "statement": "With univariate and multivariate Cox regression analysis in the survival package of R3.4.1, we screened 61 independent prognostic DEGs, and then using LR and cluster analysis, we successfully screened 11 feature DEGs: ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33823876", "locator": "sections[16] \"Discussion\" paragraph 3", "quote": "With univariate and multivariate Cox regression analysis in the survival package of R3.4.1, we screened 61 independent prognostic DEGs, and then using LR and cluster analysis, we successfully screened 11 feature DEGs: ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the [GSE65904] and [TCGA] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65904] and [https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Melanoma%20(SKCM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33823876", "locator": "sections[22] \"Availability of data and materials\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the [GSE65904] and [TCGA] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65904] and [https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Melanoma%20(SKCM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443]."}], "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:33823876"], "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:GSE65904"], "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:GSE65904"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33823876", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-021-00923-0", "sha256": "sha256:7f48ccf902231e7d464fce10c372158b057a001bedfe3ee9cb171e1bfe0f1e87", "bytes": 34201, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-021-00923-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8022370", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65904", "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=GSE65904", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65904", "version": null, "note": "The datasets supporting the conclusions of this article are available in the [GSE65904] and [TCGA] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65904] and [https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Melanoma%20(SKCM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusions of this article are available in the [GSE65904] and [TCGA] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65904] and [https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Melanoma%20(SKCM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1608593", "GSM1608594", "GSM1608595", "GSM1608596", "GSM1608597", "GSM1608598", "GSM1608599", "GSM1608600", "GSM1608601", "GSM1608602", "GSM1608603", "GSM1608604", "GSM1608605", "GSM1608606", "GSM1608607", "GSM1608608", "GSM1608609", "GSM1608610", "GSM1608611", "GSM1608612", "GSM1608613", "GSM1608614", "GSM1608615", "GSM1608616", "GSM1608617", "GSM1608618", "GSM1608619", "GSM1608620", "GSM1608621", "GSM1608622", "GSM1608623", "GSM1608624", "GSM1608625", "GSM1608626", "GSM1608627", "GSM1608628", "GSM1608629", "GSM1608630", "GSM1608631", "GSM1608632", "GSM1608633", "GSM1608634", "GSM1608635", "GSM1608636", "GSM1608637", "GSM1608638", "GSM1608639", "GSM1608640", "GSM1608641", "GSM1608642", "GSM1608643", "GSM1608644", "GSM1608645", "GSM1608646", "GSM1608647", "GSM1608648", "GSM1608649", "GSM1608650", "GSM1608651", "GSM1608652", "GSM1608653", "GSM1608654", "GSM1608655", "GSM1608656", "GSM1608657", "GSM1608658", "GSM1608659", "GSM1608660", "GSM1608661", "GSM1608662", "GSM1608663", "GSM1608664", "GSM1608665", "GSM1608666", "GSM1608667", "GSM1608668", "GSM1608669", "GSM1608670", "GSM1608671", "GSM1608672", "GSM1608673", "GSM1608674", "GSM1608675", "GSM1608676", "GSM1608677", "GSM1608678", "GSM1608679", "GSM1608680", "GSM1608681", "GSM1608682", "GSM1608683", "GSM1608684", "GSM1608685", "GSM1608686", "GSM1608687", "GSM1608688", "GSM1608689", "GSM1608690", "GSM1608691", "GSM1608692", "GSM1608693", "GSM1608694", "GSM1608695", "GSM1608696", "GSM1608697", "GSM1608698", "GSM1608699", "GSM1608700", "GSM1608701", "GSM1608702", "GSM1608703", "GSM1608704", "GSM1608705", "GSM1608706", "GSM1608707", "GSM1608708", "GSM1608709", "GSM1608710", "GSM1608711", "GSM1608712", "GSM1608713", "GSM1608714", "GSM1608715", "GSM1608716", "GSM1608717", "GSM1608718", "GSM1608719", "GSM1608720", "GSM1608721", "GSM1608722", "GSM1608723", "GSM1608724", "GSM1608725", "GSM1608726", "GSM1608727", "GSM1608728", "GSM1608729", "GSM1608730", "GSM1608731", "GSM1608732", "GSM1608733", "GSM1608734", "GSM1608735", "GSM1608736", "GSM1608737", "GSM1608738", "GSM1608739", "GSM1608740", "GSM1608741", "GSM1608742", "GSM1608743", "GSM1608744", "GSM1608745", "GSM1608746", "GSM1608747", "GSM1608748", "GSM1608749", "GSM1608750", "GSM1608751", "GSM1608752", "GSM1608753", "GSM1608754", "GSM1608755", "GSM1608756", "GSM1608757", "GSM1608758", "GSM1608759", "GSM1608760", "GSM1608761", "GSM1608762", "GSM1608763", "GSM1608764", "GSM1608765", "GSM1608766", "GSM1608767", "GSM1608768", "GSM1608769", "GSM1608770", "GSM1608771", "GSM1608772", "GSM1608773", "GSM1608774", "GSM1608775", "GSM1608776", "GSM1608777", "GSM1608778", "GSM1608779", "GSM1608780", "GSM1608781", "GSM1608782", "GSM1608783", "GSM1608784", "GSM1608785", "GSM1608786", "GSM1608787", "GSM1608788", "GSM1608789", "GSM1608790", "GSM1608791", "GSM1608792", "GSM1608793", "GSM1608794", "GSM1608795", "GSM1608796", "GSM1608797", "GSM1608798", "GSM1608799", "GSM1608800", "GSM1608801", "GSM1608802", "GSM1608803", "GSM1608804", "GSM1608805", "GSM1608806"], "sample_count": 214, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Whole-genome expression analysis of melanoma tumor biopsies from a population-based cohort.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33823876:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4e72596e23803101fb102a2933c3432f43e30220661700ced9a92b29501cf06c", "bytes": 1065, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Statistical comparison of clinical information of two types of CM samples in TCGA training data set", "structure": {"pmcid": "PMC8022370", "section_index": 3, "section_title": "Gene expression profile data and clinical information", "row_count": 11, "column_count": 4}, "table": {"label": "Table 1", "caption": "Statistical comparison of clinical information of two types of CM samples in TCGA training data set", "rows": [["Clinical characteristics", "With metastatic(N = 358)", "Without metastatic(N = 102)", "P value"], ["Age (years, mean ± sd)", "56.26 ± 15.73", "64.53 ± 13.91", "7.10E−07a"], ["Gender (Male/Female)", "226/132", "60/42", "0.488b"], ["Pathologic_M (M0/M1/–)", "313/21/24", "97/3/2", "0.317b"], ["Pathologic_N (N0/N1/N2/N3/–)", "172/65/39/44/38", "57/8/10/11/16", "0.0785b"], ["Pathologic_T (T0/T1/T2/T3/T4/–)", "23/40/72/80/67/76", "0/1/5/10/84/2", "2.2E−16b"], ["Pathologic_stage (I/II/III/IV/–)", "81/74/142/20/41", "2/65/27/3/5", "1.133E−15b"], ["Radiotherapy (Yes/No/–)", "47/310/1", "2/100/0", "4.395E−04b"], ["Tumor recurrence (Yes/No/–)", "69/135/154", "20/72/10", "0.0402b"], ["Dead (Death/Alive)", "193/165", "29/73", "0.0715b"], ["Overall survival time (months, mean ± sd)", "74.10 ± 67.91", "47.15 ± 10.04", "5.279E−22a"]], "row_count": 11, "column_count": 4, "numeric_cells": 32, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33823876:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0cb1d9472fc723df05d08bb8a3e370912ec5c632d565fbc9ba48365b20e9016a", "bytes": 1128, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "Statistical comparison of clinical information among samples in clusters based on DEGs expression levels", "structure": {"pmcid": "PMC8022370", "section_index": 10, "section_title": "DEG screening", "row_count": 12, "column_count": 4}, "table": {"label": "Table 2", "caption": "Statistical comparison of clinical information among samples in clusters based on DEGs expression levels", "rows": [["Clinical characteristics", "Cluster 1 (N = 247)", "Cluster 2 (N = 213)", "P value"], ["Age (years, mean ± sd)", "54.96 ± 15.41", "61.74 ± 15.29", "3.07E−06a"], ["Gender (Male/Female)", "152/95", "134/79", "0.773b"], ["Pathologic_M (M0/M1/–)", "219/14/14", "191/10/12", "0.679b"], ["Pathologic_N (N0/N1/N2/N3/–)", "118/42/28/33/26", "111/31/21/22/28", "0.599b"], ["Pathologic_T (T0/T1/T2/T3/T4/–)", "20/33/51/54/44/45", "3/8/26/36/107/33", "2.893E−13b"], ["Pathologic_stage (I/II/III/IV/–)", "66/43/97/14/27", "17/96/72/9/19", "6.568E−12b"], ["Radiotherapy (Yes/No/–)", "35/212/0", "14/198/1", "0.00975b"], ["Tumor recurrence (Yes/No/–)", "45/107/95", "44/100/69", "0.899b"], ["Tumor metastatic (Yes/No)", "235/12", "123/90", "2.200E−16b"], ["Dead (Death/Alive)", "111/136", "111/102", "0.149b"], ["Overall survival time (months, mean ± sd)", "78.21 ± 71.12", "42.07 ± 49.53", "4.269E−10a"]], "row_count": 12, "column_count": 4, "numeric_cells": 35, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:33823876:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:794d0671121e30a92382592a188603662a8fe2f46adadee4940f6043b1a9b368", "bytes": 759, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab3", "version": null, "note": "List of important prognostic feature DEGs screened by Logit model", "structure": {"pmcid": "PMC8022370", "section_index": 12, "section_title": "Screening of feature DEGs by LR", "row_count": 12, "column_count": 5}, "table": {"label": "Table 3", "caption": "List of important prognostic feature DEGs screened by Logit model", "rows": [["Gene", "B", "SE", "Df", "P value"], ["ZNF750", "− 7.07556", "3.11741", "1", "0.02323"], ["NLRP6", "− 3.81707", "1.92378", "1", "0.04724"], ["TGM3", "− 3.63216", "1.08106", "1", "0.00078"], ["KRTDAP", "− 1.36009", "0.65739", "1", "0.03855"], ["CAMSAP3", "− 1.18449", "0.52553", "1", "0.0242"], ["KRT6C", "− 0.96555", "0.44870", "1", "0.03141"], ["CALML5", "1.47087", "0.57774", "1", "0.0109"], ["SPRR2E", "1.59208", "0.53097", "1", "0.00271"], ["CD3G", "4.12233", "1.77857", "1", "0.02046"], ["RTP5", "7.35929", "2.91801", "1", "0.01167"], ["FAM83C", "9.35699", "3.95983", "1", "0.01813"]], "row_count": 12, "column_count": 5, "numeric_cells": 46, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:33823876:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:87d14b555f0fe92386db6ef490abeaeb0cd80a021c9dc93e847383619e2c766f", "bytes": 562, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#Tab4", "version": null, "note": "Fuzzy matrix of LR classification result", "structure": {"pmcid": "PMC8022370", "section_index": 12, "section_title": "Screening of feature DEGs by LR", "row_count": 10, "column_count": 5}, "table": {"label": "Table 4", "caption": "Fuzzy matrix of LR classification result", "rows": [["Dataset name", "Predict"], ["Class", "Metastatic", "Primary", "Percent"], ["TCGA dataset", "Observed", "", "", ""], ["", "Metastatic", "350", "8", "97.77"], ["", "Primary", "25", "77", "75.49"], ["Overall percent", "", "", "", "92.83"], ["GSE65904 microarray dataset", "Observed", "", "", ""], ["", "Metastatic", "72", "11", "86.75"], ["", "Primary", "27", "40", "59.70"], ["Overall percent", "", "", "", "74.67"]], "row_count": 10, "column_count": 5, "numeric_cells": 15, "header_rows": 2, "locator": "section[12]/table-wrap[2]#Tab4"}}, {"id": "asset:table:pmid:33823876:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d962b543c14bd65d6156a4c95f17a5b2c32b48042561aab433f1f37b28c39cb", "bytes": 2747, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab5", "version": null, "note": "GO biological processes and KEGG signaling pathways in which genes are significantly related in the interaction network", "structure": {"pmcid": "PMC8022370", "section_index": 15, "section_title": "GO and KEGG signaling pathway enrichment analysis", "row_count": 31, "column_count": 5}, "table": {"label": "Table 5", "caption": "GO biological processes and KEGG signaling pathways in which genes are significantly related in the interaction network", "rows": [["Category", "Term", "Count", "Gene", "P value"], ["Biology Process", "GO:0,031,424 ~ keratinization", "20", "TGM3, HRNR", "3.18E−35"], ["", "GO:0,008,544 ~ epidermis development", "22", "CALML5, ZNF750", "9.46E−34"], ["", "GO:0,030,216 ~ keratinocyte differentiation", "19", "TGM3, TP63", "1.04E−28"], ["", "GO:0,018,149 ~ peptide cross-linking", "14", "LCE5A, EVPL", "8.98E−22"], ["", "GO:0,061,436 ~ establishment of skin barrier", "9", "HRNR, FLG", "2.25E−16"], ["", "GO:0,045,104 ~ intermediate filament cytoskeleton organization", "4", "KRT6C, KRT3", "2.92E−06"], ["", "GO:0,043,163 ~ cell envelope organization", "3", "HRNR, TGM3", "4.98E−06"], ["", "GO:0,016,337 ~ single organismal cell–cell adhesion", "6", "PKP1, DSG1", "5.90E−06"], ["", "GO:0,042,060 ~ wound healing", "5", "NLRP6, KRT6A", "3.26E−05"], ["", "GO:0,045,109 ~ intermediate filament organization", "3", "KRT17, KRT2", "1.92E−04"], ["", "GO:0,030,855 ~ epithelial cell differentiation", "4", "KRT14, KRT3", "2.99E−04"], ["", "GO:0,007,010 ~ cytoskeleton organization", "5", "KRT6B, KRT5", "4.34E−04"], ["", "GO:0,031,069 ~ hair follicle morphogenesis", "3", "KRT17, TGM3", "5.47E−04"], ["", "GO:0,010,482 ~ regulation of epidermal cell division", "2", "TP63, SFN", "1.23E−03"], ["", "GO:0,045,110 ~ intermediate filament bundle assembly", "2", "PKP1, KRT14", "1.23E−03"], ["", "GO:0,051,546 ~ keratinocyte migration", "2", "KRT16, KRT2", "2.04E−03"], ["", "GO:0,045,087 ~ innate immune response", "6", "NLRP6,SH2D1A", "3.18E−03"], ["", "GO:0,010,838 ~ positive regulation of keratinocyte proliferation", "2", "TGM1, TP63", "3.64E−03"], ["", "GO:0,003,334 ~ keratinocyte development", "2", "KRT2, SFN", "4.04E−03"], ["", "GO:0,031,581 ~ hemidesmosome assembly", "2", "KRT, KRT14", "4.82E−03"], ["", "GO:0,043,616 ~ keratinocyte proliferation", "2", "TP63, KRT2", "4.82E−03"], ["KEGG Pathway", "hsa04020:Calcium signaling pathway", "3", "CALML3, CALML5", "9.31E−03"], ["", "hsa04070:Phosphatidylinositol signaling system", "2", "CALML3, CALML5", "1.98E−02"], ["", "hsa04640:Hematopoietic cell lineage", "2", "CD3G, IL7R", "2.26E−02"], ["", "hsa04912:GnRH signaling pathway", "2", "CALML3, CALML5", "2.53E−02"], ["", "hsa04916:Melanogenesis", "2", "CALML3, CALML5", "2.56E−02"], ["", "hsa04114:Oocyte meiosis", "2", "CALML3, CALML5", "2.80E−02"], ["", "hsa04270:Vascular smooth muscle contraction", "2", "CALML3, CALML5", "2.84E−02"], ["", "hsa04722:Neurotrophin signaling pathway", "2", "CALML3, CALML5", "3.10E−02"], ["", "hsa04910:Insulin signaling pathway", "2", "CALML3, CALML5", "3.32E−02"]], "row_count": 31, "column_count": 5, "numeric_cells": 101, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab5"}}], "gaps": ["asset:data:geo:GSE65904 not downloaded", "asset:data:geo:GSE65904 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "With univariate and multivariate Cox regression analysis in the survival package of R3.4.1, we screened 61 independent prognostic DEGs, and then using LR and cluster analysis, we successfully screened 11 feature DEGs: ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C."}}, {"id": "method-2", "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": "KM"}}, {"id": "method-3", "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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-4", "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-5", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-6", "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"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE65904"], "resolved_accessions": ["GSE65904"], "statements": ["The datasets supporting the conclusions of this article are available in the [GSE65904] and [TCGA] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65904] and [https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Melanoma%20(SKCM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443]."], "basis": "The paper names GSE65904 in GSE65904 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:33823876", "data:geo:GSE65904", "asset:table:pmid:33823876:1", "asset:table:pmid:33823876:2", "asset:table:pmid:33823876:3", "asset:table:pmid:33823876:4", "asset:table:pmid:33823876:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65904"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28075, "completion_tokens": 2010, "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:33823876", "type": "paper", "label": "pmid:33823876"}, {"id": "source:pmid:33823876", "type": "manuscript", "label": "PMID 33823876 full text"}, {"id": "data:geo:GSE65904", "type": "dataset", "label": "GEO GSE65904"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33823876", "type": "paper", "label": "pmid:33823876"}, {"id": "source:pmid:33823876", "type": "manuscript", "label": "PMID 33823876 full text"}, {"id": "data:geo:GSE65904", "type": "dataset", "label": "GEO GSE65904"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33823876", "type": "extraction", "used": ["source:pmid:33823876"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65904", "type": "accession_resolution", "used": ["data:geo:GSE65904"], "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:33823876", "parent_hash": "sha256:f40fd183441ee978a3927f434ae02f455cdd7636ce9f78acf449da391d49c95c", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE65904 licence not read", "asset:data:geo:GSE65904 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["With univariate and multivariate Cox regression analysis in the survival package of R3.4.1, we screened 61 independent prognostic DEGs, and then using LR and cluster analysis, we successfully screened 11 feature DEGs: ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C."], "order_basis": "analysis_only", "id": "assay:1"}]}