Integrative Analyses of Genes Associated with Hashimoto's Thyroiditis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34493981", "kind": "science-record", "revision": 8, "content_hash": "sha256:6dcb82ad201dca460cb13f399bebaf73771c55cf137f9372508248160afef436", "created_at": "2026-11-01T15:41:51Z", "updated_at": "2026-11-01T22:47:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative Analyses of Genes Associated with Hashimoto's Thyroiditis.", "doi": "10.1155/2021/8263829", "pmid": "34493981", "authors": ["Kangli Qiu", "Kai Li", "Tianshu Zeng", "Yunfei Liao", "Jie Min", "Nan Zhang", "Miaomiao Peng", "Wen Kong", "Lu-Lu Chen"], "journal": "Journal of immunology research", "year": 2021, "abstract": "OBJECTIVE: Hashimoto's thyroiditis, also known as chronic lymphocytic thyroiditis, is a common autoimmune thyroiditis, which mostly occurs in young and middle-aged women. It can be manifested as hyperthyroidism in the early stage; hypothyroidism may appear with the progression of the disease. Studies have shown that multiple factors such as heredity, environment, and autoimmunity are involved in the pathogenesis, but the specific mechanism is not clear. In our study, we tried to find key genes and potential molecular mechanisms of Hashimoto's thyroiditis to provide new ideas for the therapeutic targets of Hashimoto's thyroiditis.\nMETHOD: GSE138198 and GSE54958 were downloaded from the GEO database, and two datasets were combined for analysis. The combined data were normalized to identify the differentially expressed genes (DEGs), and GO and KEGG enrichment analyses were performed. Protein-protein interaction (PPI) networks and hub genes between DEGs were identified. We also used the miRWalk database to identify regulatory miRNAs associated with expressions of DEGs.\nRESULT: We identified 182 DEGs (160 upregulated and 22 downregulated) between Hashimoto's disease patients and the healthy control group. GO analysis showed that DEGs were mostly concentrated in detection of chemical stimulus involved in sensory perception, intermediate filament cytoskeleton, and olfactory receptor activity. KEGG pathway analysis showed that DEGs were mainly related to olfactory transduction. Some members of the KRTAP family and HTR5A, KNG1, DRD3, HTR1D, TAS2R16, INSL5, TAS2R42, and GRM7 are the most important hub genes in the PPI network. In addition, we recognized that OTUD4, LLPH, and ECHDC1 were the most important hub genes in the miRNA-target gene network.\nCONCLUSION: In this study, a series of bioinformatics analyses of DEGs were performed to identify the key genes and pathways associated with Hashimoto's thyroiditis. These genes and pathways provide a more detailed understanding of the pathogenesis of Hashimoto's disease and provide new ideas for the therapeutic targets of Hashimoto's thyroiditis.", "claims": [{"id": "claim-method", "statement": "The GSE138198 and GSE54958 raw datasets were evaluated using the limma R package, and the two datasets were merged for joint analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34493981", "locator": "sections[4] \"2.2. Data Processing\" paragraph 2", "quote": "The GSE138198 and GSE54958 raw datasets were evaluated using the limma R package, and the two datasets were merged for joint analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34493981", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "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:34493981"], "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:GSE138198"], "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:GSE138198"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34493981", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/8263829", "sha256": "sha256:9639bec1ff662bb01f90a4bb576b010b9bc406c7bb501710234c26a6fdba9bd9", "bytes": 18641, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/8263829", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8418929", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE138198", "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=GSE138198", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE138198", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4101749", "GSM4101750", "GSM4101751", "GSM4101752", "GSM4101753", "GSM4101754", "GSM4101755", "GSM4101756", "GSM4101757", "GSM4101758", "GSM4101759", "GSM4101760", "GSM4101761", "GSM4101762", "GSM4101763", "GSM4101764", "GSM4101765", "GSM4101766", "GSM4101767", "GSM4101768", "GSM4101769", "GSM4101770", "GSM4101771", "GSM4101772", "GSM4101773", "GSM4101774", "GSM4101775", "GSM4101776", "GSM4101777", "GSM4101778", "GSM4101779", "GSM4101780", "GSM4101781", "GSM4101782", "GSM4101783", "GSM4101784"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Differentially expression profiling in Hashimoto's thyroiditis (HT), papillary thyroid carcinoma (PTC) with HT in background, PTC without HT in background, micro PTC (mPTC), and three normal thyroid samples (TN).", "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:GSE54958", "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=GSE54958", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54958", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1327231", "GSM1327232", "GSM1327233", "GSM1327234", "GSM1327235", "GSM1327236", "GSM1327237", "GSM1327238", "GSM1327239", "GSM1327240", "GSM1327241", "GSM1327242", "GSM1327243", "GSM1327244", "GSM1327245", "GSM1327246", "GSM1327247", "GSM1327248", "GSM1327249", "GSM1327250", "GSM1327251", "GSM1327252", "GSM1327253", "GSM1327254", "GSM1327255", "GSM1327256", "GSM1327257", "GSM1327258", "GSM1327259", "GSM1327260", "GSM1327261", "GSM1327262", "GSM1327263", "GSM1327264", "GSM1327265", "GSM1327266", "GSM1327267", "GSM1327268", "GSM1327269", "GSM1327270", "GSM1327271", "GSM1327272", "GSM1327273", "GSM1327274", "GSM1327275"], "sample_count": 45, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression profiling in proliferative thyroid lesions of different histologies and normal thyroid tissue", "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:GSE138198 not downloaded", "asset:data:geo:GSE138198 licence not read", "asset:data:geo:GSE54958 not downloaded", "asset:data:geo:GSE54958 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "verbatim", "quote": "The GSE138198 and GSE54958 raw datasets were evaluated using the limma R package, and the two datasets were merged for joint analysis."}}, {"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": "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE138198", "GSE54958"], "resolved_accessions": ["GSE138198", "GSE54958"], "statements": ["The data used to support the findings of this study are included within the article."], "basis": "The paper names GSE138198, GSE54958 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34493981", "data:geo:GSE138198"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE138198"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:23Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 14928, "completion_tokens": 1048, "cached_tokens": 777}}, "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:34493981", "type": "paper", "label": "pmid:34493981"}, {"id": "source:pmid:34493981", "type": "manuscript", "label": "PMID 34493981 full text"}, {"id": "data:geo:GSE138198", "type": "dataset", "label": "GEO GSE138198"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34493981", "type": "paper", "label": "pmid:34493981"}, {"id": "source:pmid:34493981", "type": "manuscript", "label": "PMID 34493981 full text"}, {"id": "data:geo:GSE138198", "type": "dataset", "label": "GEO GSE138198"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34493981", "type": "extraction", "used": ["source:pmid:34493981"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE138198", "type": "accession_resolution", "used": ["data:geo:GSE138198"], "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:34493981", "parent_hash": "sha256:30f399a1ca1d6dc30c5c9f77567f39817aecc912700f22e5a8cc4a7ccde21fd7", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE138198 licence not read", "asset:data:geo:GSE138198 not downloaded", "asset:data:geo:GSE54958 licence not read", "asset:data:geo:GSE54958 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The GSE138198 and GSE54958 raw datasets were evaluated using the limma R package, and the two datasets were merged for joint analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}