Investigation and confirmation of differentially expressed miRNAs, as well as target gene prediction in papillary thyroid cancer, with a special emphasis on the autophagy signaling pathway.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36777002", "kind": "science-record", "revision": 3, "content_hash": "sha256:275f242e2f36ee3114d9b0a0546fcd7cb847a4e31ca8a939d442b6590d1f4c10", "created_at": "2026-11-01T19:01:21Z", "updated_at": "2026-11-01T22:08:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation and confirmation of differentially expressed miRNAs, as well as target gene prediction in papillary thyroid cancer, with a special emphasis on the autophagy signaling pathway.", "doi": "10.22099/mbrc.2022.43844.1751", "pmid": "36777002", "authors": ["Mojtaba Zehtabi", "Zahra Akbarpour", "Sepehr Valizadeh", "Yousef Roosta", "Amir Mahdi Khamaneh", "Mortaza Raeisi"], "journal": "Molecular biology research communications", "year": 2022, "abstract": "Papillary thyroid carcinoma (PTC) is the most common endocrine cancer. However, the role of biomechanics in the development and progression of PTC is obscure. The microarray dataset GSE104005 was examined to identify important microRNAs (miRNAs or miRs) and their probable roles in the carcinogenesis of PTC. The gene expression omnibus (GEO) database was used to obtain the data. R was used to access the differentially expressed miRNAs (DEMs) and genes (DEGs). The multiMiR software was used to predict DEM targets. To validate the top DEMs and DEGs, thirty tissue samples were obtained from PTC patients who had their thyroids removed and compared with 30 normal samples. The total RNA content of the tumor and corresponding non-tumoral adjacent samples were purified and converted to cDNA. Expression levels of top dysregulated miRNAs and their target and predicted DEG were evaluated using the RT-qPCR method. miR-182 and miR-183 were top upregulated miRs and miR-30d was the most downregulated miR among DEMs. Furthermore, FOXO1 which was shown to be targeted by aforementioned miRNAs, was the most downregulated genes among other DEGs. 10 hub nodes were detected by PPI construction. PTEN was the hub node with highest score. The in vitro gene expression analysis was also showed the same expression pattern in tissues. Significant increase in miR-182-5p and miR-183-5p expressions, as well as a significant decrease in FOXO1 and miR-30d-5p expressions, suggest that PTC cells may tend to preserve their autophagy capability.", "claims": [{"id": "claim-method", "statement": "Gene expression analysis was performed using ΔΔCt method, where ΔΔCt = ΔCt (Ct target gene – ΔCt ref. housekeeping gene; treated sample) - (Ct target gene – Ct ref. gene; untreated control) [11]. To compare target and reference gene expression levels, Ct values were utilized, and fold changes reflected relative quantification. The Shapiro-Wilk test was used to check the data for normality. A paired t-test was used because the data distribution of FOXO1, miR-182-5p, miR-183-5p, and miR-30d-5p was normal. A p-value of less than 0.05 was deemed significant. Statistical analyzes and boxplot creations were performed using GraphPad Prism software version 8.0.2. Finally, the significance of correlations between the fold changes (FCs) of FOXO1 and miRNA levels were calculated using Pearson's r.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36777002", "locator": "sections[2] \"MATERIALS AND METHODS\" paragraph 11", "quote": "Gene expression analysis was performed using ΔΔCt method, where ΔΔCt = ΔCt (Ct target gene – ΔCt ref. housekeeping gene; treated sample) - (Ct target gene – Ct ref. gene; untreated control) [11]. To compare target and reference gene expression levels, Ct values were utilized, and fold changes reflected relative quantification. The Shapiro-Wilk test was used to check the data for normality. A paired t-test was used because the data distribution of FOXO1, miR-182-5p, miR-183-5p, and miR-30d-5p was normal. A p-value of less than 0.05 was deemed significant. Statistical analyzes and boxplot creations were performed using GraphPad Prism software version 8.0.2. Finally, the significance of correlations between the fold changes (FCs) of FOXO1 and miRNA levels were calculated using Pearson's r."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microRNA expression profile GSE104005 was downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih. gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36777002", "locator": "sections[2] \"MATERIALS AND METHODS\" paragraph 2", "quote": "The microRNA expression profile GSE104005 was downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih. gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "FOXO1 mRNA expression was 2.66-fold lower in PTC tissues than in adjacent normal tissues, with p<0.0001.", "kind": "quantitative", "target": {"value": 2.66, "unit": "fold change", "tolerance": null, "source": "By analysis of FOXO1 mRNA levels in the PTC and adjacent normal tissues, a 2.66-fold decrease in the expression levels of FOXO1 was observed in the PTC samples in comparison with adjacent normal tissues."}, "evidence": [{"asset": "source:pmid:36777002", "locator": "sections[3] \"RESULTS\" paragraph 11", "quote": "By analysis of FOXO1 mRNA levels in the PTC and adjacent normal tissues, a 2.66-fold decrease in the expression levels of FOXO1 was observed in the PTC samples in comparison with adjacent normal tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "FOXO1 mRNA expression was 2.66-fold lower in PTC tissues than in adjacent normal tissues, with p<0.0001.", "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:36777002"], "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:GSE104005"], "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:GSE104005"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36777002", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.22099/mbrc.2022.43844.1751", "sha256": "sha256:6049f5b090ebf7011df7762732a0ce2bb16e0d49a6675e49439d0499ad12464c", "bytes": 18462, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.22099/mbrc.2022.43844.1751", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9905749", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE104005", "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=GSE104005", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104005", "version": null, "note": "The microRNA expression profile GSE104005 was downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih. gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microRNA expression profile GSE104005 was downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih. gov/geo/).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2787612", "GSM2787613", "GSM2787614", "GSM2787615", "GSM2787616", "GSM2787617", "GSM2787618", "GSM2787619", "GSM2787620", "GSM2787621", "GSM2787622", "GSM2787623", "GSM2787624", "GSM2787625", "GSM2787626", "GSM2787627", "GSM2787628", "GSM2787629", "GSM2787630", "GSM2787631", "GSM2787632", "GSM2787633", "GSM2787634", "GSM2787635", "GSM2787636", "GSM2787637", "GSM2787638", "GSM2787639", "GSM2787640", "GSM2787641", "GSM2787642", "GSM2787643", "GSM2787644", "GSM2787645"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "miRNA and gene expression profiling in human thyroid carcinomas and non-neoplastic thyroids [RNA]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE104005 not downloaded", "asset:data:geo:GSE104005 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-3", "family": null, "specific": null, "label": "ΔΔCt relative quantification with a paired t-test, and Pearson's r for correlations between fold changes", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Gene expression analysis was performed using ΔΔCt method, where ΔΔCt = ΔCt (Ct target gene – ΔCt ref. housekeeping gene; treated sample) - (Ct target gene – Ct ref. gene; untreated control) [11]. 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The microarray dataset GSE104005 was examined to identify i"], "order_basis": "paper_text_order:308", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["t and predicted DEG were evaluated using the RT-qPCR method. miR-182 and miR-183 were top upregul", "nd predicted DEG were evaluated using the RT-qPCR method. miR-182 and miR-183 were top upregul", "ehydrogenase) and U6 gene, respectively. All RT-qPCR assays were complemented triplicate. Primer", "ping gene are tabled in Table 2. 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