RARRES1 identified by comprehensive bioinformatic analysis and experimental validation as a promising biomarker in Skin Cutaneous Melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38898266", "kind": "science-record", "revision": 4, "content_hash": "sha256:f3163488191ec090433a1400da88b5ef88c7e429e6dbea6785a0b8fadd45181f", "created_at": "2026-11-01T20:28:58Z", "updated_at": "2026-11-01T22:54:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RARRES1 identified by comprehensive bioinformatic analysis and experimental validation as a promising biomarker in Skin Cutaneous Melanoma.", "doi": "10.1038/s41598-024-65032-1", "pmid": "38898266", "authors": ["Meng Liu", "Ruimin Bai", "Guanfei Zhang", "Xinyi Liu", "Ziyang Wang", "Ke He", "Xinyi Gan", "Xiaolin Zhou", "Pan Yin", "Yan Zheng", "Guorong Wang"], "journal": "Scientific reports", "year": 2024, "abstract": "Skin cutaneous melanoma (SKCM) is a highly malignant form of skin cancer, known for its unfavorable prognosis and elevated mortality rate. RARRES1, a gene responsive to retinoic acid receptors, displays varied functions in various cancer types. However, the specific role and underlying mechanisms of RARRES1 in SKCM are still unclear. GSE15605 was utilized to analyze the expression of RARRES1 in SKCM. Subsequently, the TCGA and GEO databases were employed to investigate the relationships between RARRES1 and clinicopathological parameters, as well as the prognostic implications and diagnostic efficacy of RARRES1 in SKCM. GO, KEGG, and GSEA analyses were conducted to explore the potential functions of RARRES1. Furthermore, the associations between RARRES1 and immune infiltration were examined. Genomic alterations and promoter methylation levels of RARRES1 in SKCM were assessed using cBioPortal, UALCAN, and the GEO database. Finally, RARRES1 expression in SKCM was validated through immunohistochemistry, and its functional role in SKCM progression was elucidated via in vivo and in vitro experiments. We found that RARRES1 was downregulated in SKCM compared with normal tissues, and this low expression was associated with worse clinicopathological features and poor prognosis of SKCM. The diagnostic efficacy of RARRES1, as determined by ROC analysis, was 0.732. Through GO, KEGG, and GSEA enrichment analysis, we identified 30 correlated genes and pathways that were mainly enriched in the tumor immune microenvironment, proliferation, apoptosis, and autophagy. Additionally, RARRES1 expression was found to be positively related to the infiltration of various immune cells in SKCM, particularly macrophages and T helper cells, among others. Analysis of genomic alterations and promoter methylation revealed that shallow deletion and hypermethylation of the RARRES1 promoter could lead to reduced RARRES1 expression. IHC validation confirmed the downregulation of RARRES1 in SKCM. Moreover, overexpression of RARRES1 inhibited the proliferation and migration of A375 cells, promoted apoptosis, and inhibited autophagic flux. In the mouse xenograft model, RARRES1 overexpression also suppressed SKCM tumor growth. Collectively, these findings suggest that RARRES1 may function as a suppressor and could potentially serve as a prognostic biomarker and therapeutic target for SKCM.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival curves were constructed to compare the prognosis between the high and low RARRES1 groups. Additionally, univariate and multivariate Cox regression analyses were employed to assess the risk factors associated with SKCM. For the ROC analysis, the expression data of RARRES1 in the GSE15605 dataset was processed by Graphpad prism.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38898266", "locator": "sections[4] \"Prognostic analysis\" paragraph 2", "quote": "Kaplan–Meier survival curves were constructed to compare the prognosis between the high and low RARRES1 groups."}, {"asset": "source:pmid:38898266", "locator": "sections[4] \"Prognostic analysis\" paragraph 2", "quote": "Additionally, univariate and multivariate Cox regression analyses were employed to assess the risk factors associated with SKCM."}, {"asset": "source:pmid:38898266", "locator": "sections[4] \"Prognostic analysis\" paragraph 2", "quote": "For the ROC analysis, the expression data of RARRES1 in the GSE15605 dataset was processed by Graphpad prism."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38898266", "locator": "sections[41] \"Data availability\" paragraph 2", "quote": "The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RARRES1 showed diagnostic performance for SKCM, with a ROC AUC of 0.732 (P = 0.0048), while low expression was associated with adverse clinical features and poor prognosis.", "kind": "quantitative", "target": {"value": 0.0048, "unit": "p-value", "tolerance": null, "source": "Based on the expression data of RARRES1 in GSE15605, the diagnostic value of RARRES1 in SKCM was calculated, the area under the curve (AUC) was 0.732 (P = 0.0048), which illustrated that RARRES1 had a good diagnostic performance in SKCM21 (Fig. 1N)."}, "evidence": [{"asset": "source:pmid:38898266", "locator": "sections[27] \"Expression, clinicopathological correlation, prognostic and diagnostic potential of RARRES1 in SKCM\" paragraph 2", "quote": "Based on the expression data of RARRES1 in GSE15605, the diagnostic value of RARRES1 in SKCM was calculated, the area under the curve (AUC) was 0.732 (P = 0.0048), which illustrated that RARRES1 had a good diagnostic performance in SKCM21 (Fig. 1N)."}, {"asset": "source:pmid:38898266", "locator": "sections[27] \"Expression, clinicopathological correlation, prognostic and diagnostic potential of RARRES1 in SKCM\" paragraph 2", "quote": "The Kaplan–Meier survival analysis indicated that low expression of RARRES1 was associated with unfavorable overall survival (OS) or disease specific survival (DSS) (Fig. 1I–J)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "RARRES1 showed diagnostic performance for SKCM, with a ROC AUC of 0.732 (P = 0.0048), while low expression was associated with adverse clinical features and poor prognosis.", "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:38898266"], "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:GSE120878"], "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:GSE120878"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38898266", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-65032-1", "sha256": "sha256:88b626db84a0b0faf8380e850377804fb2a81410dc0a59859bf088251568b444", "bytes": 55380, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-65032-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11187141", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE120878", "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=GSE120878", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE120878", "version": null, "note": "The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3417545", "GSM3417546", "GSM3417547", "GSM3417548", "GSM3417549", "GSM3417550", "GSM3417551", "GSM3417552", "GSM3417553", "GSM3417554", "GSM3417555", "GSM3417556", "GSM3417557", "GSM3417558", "GSM3417559", "GSM3417560", "GSM3417561", "GSM3417562", "GSM3417563", "GSM3417564", "GSM3417565", "GSM3417566", "GSM3417567", "GSM3417568", "GSM3417569", "GSM3417570", "GSM3417571", "GSM3417572", "GSM3417573", "GSM3417574", "GSM3417575", "GSM3417576", "GSM3417577", "GSM3417578", "GSM3417579", "GSM3417580", "GSM3417581", "GSM3417582", "GSM3417583", "GSM3417584", "GSM3417585", "GSM3417586", "GSM3417587", "GSM3417588", "GSM3417589", "GSM3417590", "GSM3417591", "GSM3417592", "GSM3417593", "GSM3417594", "GSM3417595", "GSM3417596", "GSM3417597", "GSM3417598", "GSM3417599", "GSM3417600", "GSM3417601", "GSM3417602", "GSM3417603", "GSM3417604", "GSM3417605", "GSM3417606", "GSM3417607", "GSM3417608", "GSM3417609", "GSM3417610", "GSM3417611", "GSM3417612", "GSM3417613", "GSM3417614", "GSM3417615", "GSM3417616", "GSM3417617", "GSM3417618", "GSM3417619", "GSM3417620", "GSM3417621", "GSM3417622", "GSM3417623", "GSM3417624", "GSM3417625", "GSM3417626", "GSM3417627", "GSM3417628", "GSM3417629", "GSM3417630", "GSM3417631", "GSM3417632", "GSM3417633", "GSM3417634", "GSM3417635", "GSM3417636", "GSM3417637", "GSM3417638", "GSM3417639", "GSM3417640", "GSM3417641", "GSM3417642", "GSM3417643", "GSM3417644", "GSM3417645", "GSM3417646", "GSM3417647", "GSM3417648", "GSM3417649", "GSM3417650", "GSM3417651", "GSM3417652", "GSM3417653", "GSM3417654", "GSM3417655", "GSM3417656", "GSM3417657", "GSM3417658", "GSM3417659", "GSM3417660", "GSM3417661", "GSM3417662", "GSM3417663", "GSM3417664", "GSM3417665", "GSM3417666", "GSM3417667", "GSM3417668", "GSM3417669", "GSM3417670", "GSM3417671", "GSM3417672", "GSM3417673", "GSM3417674", "GSM3417675", "GSM3417676", "GSM3417677", "GSM3417678", "GSM3417679", "GSM3417680", "GSM3417681", "GSM3417682", "GSM3417683", "GSM3417684", "GSM3417685", "GSM3417686", "GSM3417687", "GSM3417688", "GSM3417689", "GSM3417690", "GSM3417691", "GSM3417692", "GSM3417693", "GSM3417694", "GSM3417695", "GSM3417696", "GSM3417697", "GSM3417698", "GSM3417699", "GSM3417700", "GSM3417701", "GSM3417702", "GSM3417703", "GSM3417704", "GSM3417705", "GSM3417706"], "sample_count": 162, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Identification of a robust methylation classifier for cutaneous melanoma diagnosis", "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:GSE15605", "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=GSE15605", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15605", "version": null, "note": "The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM390208", "GSM390209", "GSM390210", "GSM390211", "GSM390212", "GSM390213", "GSM390214", "GSM390215", "GSM390216", "GSM390217", "GSM390218", "GSM390219", "GSM390220", "GSM390221", "GSM390222", "GSM390223", "GSM390224", "GSM390225", "GSM390226", "GSM390227", "GSM390228", "GSM390229", "GSM390230", "GSM390231", "GSM390232", "GSM390233", "GSM390234", "GSM390235", "GSM390236", "GSM390237", "GSM390238", "GSM390239", "GSM390240", "GSM390241", "GSM390242", "GSM390243", "GSM390244", "GSM390245", "GSM390246", "GSM390247", "GSM390248", "GSM390249", "GSM390250", "GSM390251", "GSM390252", "GSM390253", "GSM390254", "GSM390255", "GSM390256", "GSM390257", "GSM390258", "GSM390259", "GSM390260", "GSM390261", "GSM390262", "GSM390263", "GSM390264", "GSM390265", "GSM390266", "GSM390267", "GSM390268", "GSM390269", "GSM390270", "GSM390271", "GSM390272", "GSM390273", "GSM390274", "GSM390275", "GSM390276", "GSM390277", "GSM390278", "GSM390279", "GSM390280", "GSM390281"], "sample_count": 74, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptome profiling identifies HMGA2 as a novel gene in melanoma progression", "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:GSE120878 not downloaded", "asset:data:geo:GSE120878 licence not read", "asset:data:geo:GSE15605 not downloaded", "asset:data:geo:GSE15605 licence not read"]}, "analysis": {"state": "partial", "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": "reordered", "quote": "Kaplan–Meier survival curves were constructed to compare the prognosis between the high and low RARRES1 groups. Additionally, univariate and multivariate Cox regression analyses were employed to assess the risk factors associated with SKCM. For the ROC analysis, the expression data of RARRES1 in the GSE15605 dataset was processed by Graphpad prism."}}, {"id": "method-2", "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-3", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Welch"}}, {"id": "method-4", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-5", "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": "Logrank"}}, {"id": "method-6", "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": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-7", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.0048, "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": ["method.reader_differs_from_extractor"]}, "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": ["GSE15605", "GSE120878"], "resolved_accessions": ["GSE15605", "GSE120878"], "statements": ["The datasets featured in this study are available in online repositories, and the names of these repositories along with their respective accession numbers can be located within the article. The GSE15605 and GSE120878 datasets were downloaded from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. Patient information and prognosis data of SKCM was obtained from TCGA (https://www.cancer.gov/ccg/research/genome-sequencing/tcga)."], "basis": "The paper names GSE15605, GSE120878 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": ["cox_ph"], "assets": ["source:pmid:38898266", "data:geo:GSE120878"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE120878"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:21:46Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15954, "completion_tokens": 2213, "cached_tokens": 256}}, "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:38898266", "type": "paper", "label": "pmid:38898266"}, {"id": "source:pmid:38898266", "type": "manuscript", "label": "PMID 38898266 full text"}, {"id": "data:geo:GSE120878", "type": "dataset", "label": "GEO GSE120878"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38898266", "type": "paper", "label": "pmid:38898266"}, {"id": "source:pmid:38898266", "type": "manuscript", "label": "PMID 38898266 full text"}, {"id": "data:geo:GSE120878", "type": "dataset", "label": "GEO GSE120878"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38898266", "type": "extraction", "used": ["source:pmid:38898266"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE120878", "type": "accession_resolution", "used": ["data:geo:GSE120878"], "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:38898266", "parent_hash": "sha256:f4c77a92bf6eb30ddd4eafa15ac4b731428b84456f7ba41580f329ab8e509269", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE120878 licence not read", "asset:data:geo:GSE120878 not downloaded", "asset:data:geo:GSE15605 licence not read", "asset:data:geo:GSE15605 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ES1 expression in SKCM was validated through immunohistochemistry, and its functional role in SKCM progression", "er could lead to reduced RARRES1 expression. IHC validation confirmed the downregulation of R"], "order_basis": "paper_text_order:1088", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["role in SKCM progression was elucidated via in vivo and in vitro experiments. We found that RARR", "ed apoptosis, and inhibited autophagic flux. In the mouse xenograft model, RARRES1 overexpression also", "tosis, and inhibited autophagic flux. In the mouse xenograft model, RARRES1 overexpression also"], "order_basis": "paper_text_order:1174", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["umor immune microenvironment, proliferation, apoptosis, and autophagy. Additionally, RARRES1 expres", "ration and migration of A375 cells, promoted apoptosis, and inhibited autophagic flux. In the mouse", "otic G1 Phase and G1/S transition (Fig. 2D), caspase cascade (Fig. 2E), oxidative damage response", "D) mitotic G1 phase and G1/S transition, (E) caspase cascade, (F) oxidative damage response, (G)"], "order_basis": "paper_text_order:1644", "id": "assay:3"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["a of RARRES1 in SKCM and normal samples. The RNAseq data for SKCM was acquired from the TCGA dat"], "order_basis": "paper_text_order:2808", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["The A375 cells were purchased from ATCC and cultured in Dulbecco’s modified Eagle’s medium containin"], "order_basis": "paper_text_order:4749", "id": "assay:5"}, {"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": ["Kaplan–Meier survival curves were constructed to compare the prognosis between the high and low RARRES1 groups. Additionally, univariate and multivariate Cox regression analyses were employed to assess the risk factors associated with SKCM. For the ROC analysis, the expression data of RARRES1 in the GSE15605 dataset was processed by Graphpad prism."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}