Comprehensive Analysis of the PROSER2-AS1-Related ceRNA Network and Immune Cell Infiltration in Papillary Thyroid Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35210835", "kind": "science-record", "revision": 3, "content_hash": "sha256:8f3f49ed6149d2ed38923b81d6c23338a9e6c7852a8c2b6d8a608f812dd085b1", "created_at": "2026-11-01T17:36:58Z", "updated_at": "2026-11-01T21:27:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis of the PROSER2-AS1-Related ceRNA Network and Immune Cell Infiltration in Papillary Thyroid Carcinoma.", "doi": "10.2147/IJGM.S338019", "pmid": "35210835", "authors": ["Tingting Wang", "Qian Yu", "Wei Zhang", "Li Gao"], "journal": "International journal of general medicine", "year": 2022, "abstract": "BACKGROUND: Papillary thyroid carcinoma (PTC) is a malignant tumor of the endocrine system, and distant metastasis leads to poor prognosis for patients with PTC. The competitive endogenous RNA (ceRNA) network and tumor-infiltrating immune cells might participate in tumor prognosis and distant metastasis. However, few studies have focused on ceRNAs and immune cells in PTC.\nMETHODS: We identified differentially expressed lncRNAs (DELs) using the GEO2R tool of the GEO database. Through comprehensive analysis, we selected lncRNA PROSER2-AS1 and constructed a PROSER2-AS1-mediated ceRNA network. Survival was analyzed with a Kaplan-Meier (KM) curve. Gene set enrichment analysis (GSEA) was performed to determine the function of PROSER2-AS1 in the ceRNA network using TCGA database. Moreover, the relationship between PROSER2-AS1 and immune cell infiltration was analyzed with ssGSEA using the \"GSVA\" package in R.\nRESULTS: Comprehensive analysis of the GSE66783 dataset revealed 105 significantly differentially expressed lncRNAs. Univariate and multivariate Cox regression analyses were performed to assess the prognostic significance of the DELs, and we identified lncRNA PROSER2-AS1 as an independent factor for prognosis in PTC (p < 0.05). Considering the online tools LncRNASNP2 and miRWalk3.0, we constructed a PROSER2-AS1-related ceRNA network. Furthermore, the GSEA results suggested that PROSER2-AS1 may be involved in immune cell infiltration and that PROSER2-AS1 was correlated with 14 types of tumor-infiltrating immune cells. PROSER2-AS1 might function through TGFBR3.\nCONCLUSION: lncRNA PROSER2-AS1 and related mRNAs (TGFBR3) may be potential prognostic biomarkers in PTC and may correlate with immune infiltrates.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression analysis was used to determine the effect of DELs on progression-free survival (PFS) using the survival package of R software. To identify independent prognostic factors, all significant variables on univariate Cox regression analysis (P≤0.05) were subjected to multivariate Cox regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35210835", "locator": "sections[4] \"Univariate and Multivariate Cox Analyses\" paragraph 2", "quote": "Univariate Cox regression analysis was used to determine the effect of DELs on progression-free survival (PFS) using the survival package of R software. To identify independent prognostic factors, all significant variables on univariate Cox regression analysis (P≤0.05) were subjected to multivariate Cox regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of the study are available in GEO database at https://www.ncbi.nlm.nih.gov/geo/, TCGA database at https://portal.gdc.cancer.gov/ and immune-related gene list at ImmPort (https://www.immport.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35210835", "locator": "sections[20] \"Data Sharing Statement\" paragraph 2", "quote": "The data that support the findings of the study are available in GEO database at https://www.ncbi.nlm.nih.gov/geo/, TCGA database at https://portal.gdc.cancer.gov/ and immune-related gene list at ImmPort (https://www.immport.org/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "lncRNA PROSER2-AS1 was identified as an independent factor for prognosis in PTC (p < 0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Univariate and multivariate Cox regression analyses were performed to assess the prognostic significance of the DELs, and we identified lncRNA PROSER2-AS1 as an independent factor for prognosis in PTC (p < 0.05)."}, "evidence": [{"asset": "source:pmid:35210835", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Univariate and multivariate Cox regression analyses were performed to assess the prognostic significance of the DELs, and we identified lncRNA PROSER2-AS1 as an independent factor for prognosis in PTC (p < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "lncRNA PROSER2-AS1 was identified as an independent factor for prognosis in PTC (p < 0.05).", "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:35210835"], "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:GSE66783"], "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:GSE66783"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35210835", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S338019", "sha256": "sha256:1fdf4fba2ff1377f4455c2c2806060bdeacf8a0caddfadc690478ebd0681da63", "bytes": 29730, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S338019", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8858959", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE66783", "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=GSE66783", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66783", "version": null, "note": "The data that support the findings of the study are available in GEO database at https://www.ncbi.nlm.nih.gov/geo/, TCGA database at https://portal.gdc.cancer.gov/ and immune-related gene list at ImmPort (https://www.immport.org/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of the study are available in GEO database at https://www.ncbi.nlm.nih.gov/geo/, TCGA database at https://portal.gdc.cancer.gov/ and immune-related gene list at ImmPort (https://www.immport.org/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1631910", "GSM1631911", "GSM1631912", "GSM1631913", "GSM1631914", "GSM1631915", "GSM1631916", "GSM1631917", "GSM1631918", "GSM1631919"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "19850", "taxon": "Homo sapiens", "title": "Genome-wide analysis of long noncoding RNA expression profile in papillary thyroid carcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE66783 not downloaded", "asset:data:geo:GSE66783 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": "Univariate Cox regression analysis was used to determine the effect of DELs on progression-free survival (PFS) using the survival package of R software. To identify independent prognostic factors, all significant variables on univariate Cox regression analysis (P≤0.05) were subjected to multivariate Cox regression analysis."}}, {"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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "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": ["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": ["GSE66783"], "resolved_accessions": ["GSE66783"], "statements": ["The data that support the findings of the study are available in GEO database at https://www.ncbi.nlm.nih.gov/geo/, TCGA database at https://portal.gdc.cancer.gov/ and immune-related gene list at ImmPort (https://www.immport.org/)."], "basis": "The paper names GSE66783 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:35210835", "data:geo:GSE66783"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE66783"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:35:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9754, "completion_tokens": 1506, "cached_tokens": 264}}, "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:35210835", "type": "paper", "label": "pmid:35210835"}, {"id": "source:pmid:35210835", "type": "manuscript", "label": "PMID 35210835 full text"}, {"id": "data:geo:GSE66783", "type": "dataset", "label": "GEO GSE66783"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35210835", "type": "paper", "label": "pmid:35210835"}, {"id": "source:pmid:35210835", "type": "manuscript", "label": "PMID 35210835 full text"}, {"id": "data:geo:GSE66783", "type": "dataset", "label": "GEO GSE66783"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35210835", "type": "extraction", "used": ["source:pmid:35210835"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE66783", "type": "accession_resolution", "used": ["data:geo:GSE66783"], "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:35210835", "parent_hash": "sha256:cd701cfab705cf6eef104e3ea493b75b52fc673ce87adf41943fb373bf4d30f1", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE66783 licence not read", "asset:data:geo:GSE66783 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": ["Univariate Cox regression analysis was used to determine the effect of DELs on progression-free survival (PFS) using the survival package of R software. To identify independent prognostic factors, all significant variables on univariate Cox regression analysis (P≤0.05) were subjected to multivariate Cox regression analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}