Exploring the impact of deubiquitination on melanoma prognosis through single-cell RNA sequencing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39712483", "kind": "science-record", "revision": 2, "content_hash": "sha256:027dc51cfd89e91b631b58d7a3f7a5a2de4daa2a15465f5378abe72f79347573", "created_at": "2026-11-01T20:30:02Z", "updated_at": "2026-11-01T21:34:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the impact of deubiquitination on melanoma prognosis through single-cell RNA sequencing.", "doi": "10.3389/fgene.2024.1509049", "pmid": "39712483", "authors": ["Su Peng", "Jiaheng Xie", "Xiaohu He"], "journal": "Frontiers in genetics", "year": 2024, "abstract": "Background: Cutaneous melanoma, characterized by the malignant proliferation of melanocytes, exhibits high invasiveness and metastatic potential. Thus, identifying novel prognostic biomarkers and therapeutic targets is essential.\nMethods: We utilized single-cell RNA sequencing data (GSE215120) from the Gene Expression Omnibus (GEO) database, preprocessing it with the Seurat package. Dimensionality reduction and clustering were executed through Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP). Cell types were annotated based on known marker genes, and the AUCell algorithm assessed the enrichment of deubiquitination-related genes. Cells were categorized into DUB_high and DUB_low groups based on AUCell scores, followed by differential expression analysis. Importantly, we constructed a robust prognostic model utilizing various genes, which was evaluated in the TCGA cohort and an external validation cohort.\nResults: Our prognostic model, developed using Random Survival Forest (RSF) and Ridge Regression methods, demonstrated excellent predictive performance, evidenced by high C-index and AUC values across multiple cohorts. Furthermore, analyses of immune cell infiltration and tumor microenvironment scores revealed significant differences in immune cell distribution and microenvironment characteristics between high-risk and low-risk groups. Functional experiments indicated that TBC1D16 significantly impacts the migration and proliferation of melanoma cells.\nConclusion: This study highlights the critical role of deubiquitination in melanoma and presents a novel prognostic model that effectively stratifies patient risk. The model's strong predictive ability enhances clinical decision-making and provides a framework for future studies on the therapeutic potential of deubiquitination mechanisms in melanoma progression. Further validation and exploration of this model's applicability in clinical settings are warranted.", "claims": [{"id": "claim-method", "statement": "Among the 101 combinations tested, the Random Survival Forest (RSF) combined with Ridge regression emerged as the optimal model, achieving the highest concordance index (c-index) in the validation cohort (Figure 2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39712483", "locator": "sections[19] \"Identification of the optimal prognostic model\" paragraph 3", "quote": "Among the 101 combinations tested, the Random Survival Forest (RSF) combined with Ridge regression emerged as the optimal model, achieving the highest concordance index (c-index) in the validation cohort (Figure 2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39712483", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Notably, the AUC values ranged from 0.52 to 0.85 across the cohorts, with the TCGA cohort achieving an AUC of 0.75 at the 5-year mark, indicating strong predictive capability.", "kind": "quantitative", "target": {"value": 0.75, "unit": "auc", "tolerance": null, "source": "Notably, the AUC values ranged from 0.52 to 0.85 across the cohorts, with the TCGA cohort achieving an AUC of 0.75 at the 5-year mark, indicating strong predictive capability."}, "evidence": [{"asset": "source:pmid:39712483", "locator": "sections[20] \"Survival analysis and model validation in multiple cohorts\" paragraph 4", "quote": "Notably, the AUC values ranged from 0.52 to 0.85 across the cohorts, with the TCGA cohort achieving an AUC of 0.75 at the 5-year mark, indicating strong predictive capability."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Notably, the AUC values ranged from 0.52 to 0.85 across the cohorts, with the TCGA cohort achieving an AUC of 0.75 at the 5-year mark, indicating strong predictive capability.", "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:39712483"], "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:GSE19234"], "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": {"hazard_ratio": "ied, and hazard ratios (HR) were calculated using"}, "inputs": ["data:geo:GSE19234"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39712483", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2024.1509049", "sha256": "sha256:c75264d8c5faf729a99a39a48cde21cd6a0cffd787e6448a085a4751ce842c12", "bytes": 39744, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2024.1509049", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11659643", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19234", "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=GSE19234", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19234", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM476606", "GSM476607", "GSM476608", "GSM476609", "GSM476610", "GSM476611", "GSM476612", "GSM476613", "GSM476614", "GSM476615", "GSM476616", "GSM476617", "GSM476618", "GSM476619", "GSM476620", "GSM476621", "GSM476622", "GSM476623", "GSM476624", "GSM476625", "GSM476626", "GSM476627", "GSM476628", "GSM476629", "GSM476630", "GSM476631", "GSM476632", "GSM476633", "GSM476634", "GSM476635", "GSM476636", "GSM476637", "GSM476638", "GSM476639", "GSM476640", "GSM476641", "GSM476642", "GSM476643", "GSM476644", "GSM476645", "GSM476646", "GSM476647", "GSM476648", "GSM476649"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.", "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:GSE215120", "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=GSE215120", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE215120", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6622292", "GSM6622293", "GSM6622294", "GSM6622295", "GSM6622296", "GSM6622297", "GSM6622298", "GSM6622299", "GSM6622300", "GSM6622301", "GSM6622302"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma [scRNA-Seq]", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE22153", "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=GSE22153", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22153", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM550966", "GSM550967", "GSM550968", "GSM550969", "GSM550970", "GSM550971", "GSM550972", "GSM550973", "GSM550974", "GSM550975", "GSM550976", "GSM550977", "GSM550978", "GSM550979", "GSM550980", "GSM550981", "GSM550982", "GSM550983", "GSM550984", "GSM550985", "GSM550986", "GSM550987", "GSM550988", "GSM550989", "GSM550990", "GSM550991", "GSM550992", "GSM550993", "GSM550994", "GSM550995", "GSM550996", "GSM550997", "GSM550998", "GSM550999", "GSM551000", "GSM551001", "GSM551002", "GSM551003", "GSM551004", "GSM551005", "GSM551006", "GSM551007", "GSM551008", "GSM551009", "GSM551010", "GSM551011", "GSM551012", "GSM551013", "GSM551014", "GSM551015", "GSM551016", "GSM551017", "GSM551018", "GSM551019", "GSM551020", "GSM551021", "GSM551022"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "6102", "taxon": "Homo sapiens", "title": "Gene Experssion Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome (test set)", "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:GSE59455", "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=GSE59455", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59455", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1437254", "GSM1437255", "GSM1437256", "GSM1437257", "GSM1437258", "GSM1437259", "GSM1437260", "GSM1437261", "GSM1437262", "GSM1437263", "GSM1437264", "GSM1437265", "GSM1437266", "GSM1437267", "GSM1437268", "GSM1437269", "GSM1437270", "GSM1437271", "GSM1437272", "GSM1437273", "GSM1437274", "GSM1437275", "GSM1437276", "GSM1437277", "GSM1437278", "GSM1437279", "GSM1437280", "GSM1437281", "GSM1437282", "GSM1437283", "GSM1437284", "GSM1437285", "GSM1437286", "GSM1437287", "GSM1437288", "GSM1437289", "GSM1437290", "GSM1437291", "GSM1437292", "GSM1437293", "GSM1437294", "GSM1437295", "GSM1437296", "GSM1437297", "GSM1437298", "GSM1437299", "GSM1437300", "GSM1437301", "GSM1437302", "GSM1437303", "GSM1437304", "GSM1437305", "GSM1437306", "GSM1437307", "GSM1437308", "GSM1437309", "GSM1437310", "GSM1437311", "GSM1437312", "GSM1437313", "GSM1437314", "GSM1437315", "GSM1437316", "GSM1437317", "GSM1437318", "GSM1437319", "GSM1437320", "GSM1437321", "GSM1437322", "GSM1437323", "GSM1437324", "GSM1437325", "GSM1437326", "GSM1437327", "GSM1437328", "GSM1437329", "GSM1437330", "GSM1437331", "GSM1437332", "GSM1437333", "GSM1437334", "GSM1437335", "GSM1437336", "GSM1437337", "GSM1437338", "GSM1437339", "GSM1437340", "GSM1437341", "GSM1437342", "GSM1437343", "GSM1437344", "GSM1437345", "GSM1437346", "GSM1437347", "GSM1437348", "GSM1437349", "GSM1437350", "GSM1437351", "GSM1437352", "GSM1437353", "GSM1437354", "GSM1437355", "GSM1437356", "GSM1437357", "GSM1437358", "GSM1437359", "GSM1437360", "GSM1437361", "GSM1437362", "GSM1437363", "GSM1437364", "GSM1437365", "GSM1437366", "GSM1437367", "GSM1437368", "GSM1437369", "GSM1437370", "GSM1437371", "GSM1437372", "GSM1437373", "GSM1437374", "GSM1437375", "GSM1437376", "GSM1437377", "GSM1437378", "GSM1437379", "GSM1437380", "GSM1437381", "GSM1437382", "GSM1437383", "GSM1437384", "GSM1437385", "GSM1437386", "GSM1437387", "GSM1437388", "GSM1437389", "GSM1437390", "GSM1437391", "GSM1437392", "GSM1437393", "GSM1437394"], "sample_count": 141, "group_sizes": null, "group_sizes_basis": null, "platform": "8432", "taxon": "Homo sapiens", "title": "Whole genome expression data from formalin-fixed parrafin embedded (FFPE) primary and metastatic melanomas", "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:GSE19234 not downloaded", "asset:data:geo:GSE19234 licence not read", "asset:data:geo:GSE215120 not downloaded", "asset:data:geo:GSE215120 licence not read", "asset:data:geo:GSE22153 not downloaded", "asset:data:geo:GSE22153 licence not read", "asset:data:geo:GSE59455 not downloaded", "asset:data:geo:GSE59455 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": {"hazard_ratio": "ied, and hazard ratios (HR) were calculated using"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "ied, and hazard ratios (HR) were calculated using"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "ied, and hazard ratios (HR) were calculated using"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Principal Component Analysis"}}, {"id": "method-5", "family": null, "specific": null, "label": "Random Survival Forest (RSF) combined with Ridge regression", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Among the 101 combinations tested, the Random Survival Forest (RSF) combined with Ridge regression emerged as the optimal model, achieving the highest concordance index (c-index) in the validation cohort (Figure 2)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 0.75, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["GSE215120", "GSE19234", "GSE22153", "GSE59455", "and GSE65904"], "resolved_accessions": ["GSE215120", "GSE19234", "GSE22153", "GSE59455"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE215120, GSE19234, GSE22153, GSE59455 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": ["survival_km"], "assets": ["source:pmid:39712483", "data:geo:GSE19234"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19234"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:43:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10036, "completion_tokens": 1973, "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:39712483", "type": "paper", "label": "pmid:39712483"}, {"id": "source:pmid:39712483", "type": "manuscript", "label": "PMID 39712483 full text"}, {"id": "data:geo:GSE19234", "type": "dataset", "label": "GEO GSE19234"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39712483", "type": "paper", "label": "pmid:39712483"}, {"id": "source:pmid:39712483", "type": "manuscript", "label": "PMID 39712483 full text"}, {"id": "data:geo:GSE19234", "type": "dataset", "label": "GEO GSE19234"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39712483", "type": "extraction", "used": ["source:pmid:39712483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19234", "type": "accession_resolution", "used": ["data:geo:GSE19234"], "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:39712483", "parent_hash": "sha256:0f010fbad01cc5706792a0d029df7231b5ce720eeb38ea3ed6b6977463357329", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE19234 licence not read", "asset:data:geo:GSE19234 not downloaded", "asset:data:geo:GSE215120 licence not read", "asset:data:geo:GSE215120 not downloaded", "asset:data:geo:GSE22153 licence not read", "asset:data:geo:GSE22153 not downloaded", "asset:data:geo:GSE59455 licence not read", "asset:data:geo:GSE59455 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ubiquitination on melanoma prognosis through single-cell RNA sequencing.", "c targets is essential. Methods: We utilized single-cell RNA sequencing data (GSE215120) from the Gene Expression Om", "rformed using GraphPad Prism and R software. Single-cell RNA sequencing analysis of cutaneous melanoma microenvironm", "lysis of cutaneous melanoma microenvironment Single-cell RNA sequencing analysis was performed on cutaneous melanoma"], "order_basis": "paper_text_order:26", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on on melanoma prognosis through single-cell RNA sequencing.", "essential. Methods: We utilized single-cell RNA sequencing data (GSE215120) from the Gene Expression Om", "g GraphPad Prism and R software. Single-cell RNA sequencing analysis of cutaneous melanoma microenvironm", "aneous melanoma microenvironment Single-cell RNA sequencing analysis was performed on cutaneous melanoma"], "order_basis": "paper_text_order:38", "id": "assay:2"}, {"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": "consumes_earlier_output", "id": "assay:3"}]}