Microarray Data of Lacrimal Gland Implicates Dysregulated Protein Processing in Endoplasmic Reticulum in Graves' Ophthalmopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33613444", "kind": "science-record", "revision": 9, "content_hash": "sha256:840c22a5419e0f892d638f14cd3f917322bfc9344ef497ac12fc457622e429ab", "created_at": "2026-11-01T15:41:25Z", "updated_at": "2026-11-01T22:46:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray Data of Lacrimal Gland Implicates Dysregulated Protein Processing in Endoplasmic Reticulum in Graves' Ophthalmopathy.", "doi": "10.3389/fendo.2020.571151", "pmid": "33613444", "authors": ["Wenling Tu", "Jia Yao", "Zhanjun Mei", "Xue Jiang", "Yuhong Shi"], "journal": "Frontiers in endocrinology", "year": 2020, "abstract": "Graves' ophthalmopathy (GO) has become one of the most common orbital diseases. Although some evidences announced the potential mechanism of pathological changes in extraocular muscle and orbital adipose tissue, little is known about that in lacrimal enlargement of GO patients. Thus, gene expression profiles of lacrimal gland derived from GO patients and normal controls were investigated using the microarray datasets of GSE105149 and GSE58331. The raw data and annotation files of GSE105149 and GSE58331 were downloaded from Gene Expression Omnibus (GEO) database. Bioinformatics including differentially expressed genes (DEGs), Gene Ontology, Kyoto Encyclopedia of Gene and Genome (KEGG) pathway, protein-protein interaction (PPI) network construction, hub gene identification, and gene set variation analysis (GSVA) were successively performed. A total of 173 overlapping DEGs in GSE105149 and GSE58331 were screened out, including 20 up-regulated and 153 down-regulated genes. Gene Ontology, KEGG and GSVA analyses of these DEGs showed that the most significant mechanism was closely associated with endoplasmic reticulum (ER). Moreover, we identified 40 module genes and 13 hub genes which were also enriched in the ER-associated terms and pathways. Among the hub genes, five genes including HSP90AA1, HSP90B1, DNAJC10, HSPA5, and CANX may be involved in the dysfunction of protein processing in ER. Taken together, our observations revealed a dysregulated gene network which is essential for protein processing in ER in GO patients. These findings provided a potential mechanism in the progression of lacrimal enlargement in GO patients, as a new insight into GO pathogenesis.", "claims": [{"id": "claim-method", "statement": "The Limma R package (http://www.bioconductor.org/packages/release/bioc/html/limma.html) was used to detect differentially expressed genes (DEGs) between TED and normal lacrimal group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33613444", "locator": "sections[4] \"Screening of the Differentially Expressed Genes\" paragraph 2", "quote": "The Limma R package (http://www.bioconductor.org/packages/release/bioc/html/limma.html) was used to detect differentially expressed genes (DEGs) between TED and normal lacrimal group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data and annotation files of GSE105149 and GSE58331 were downloaded from the GEO database. GSE105149 was the microarray data of various lacrimal gland tissues, including sarcoidosis, granulomatosis with polyangiitis, thyroid eye disease, nonspecific orbital inflammation and healthy controls (16).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33613444", "locator": "sections[3] \"Characteristics of the Microarray Data Sets\" paragraph 2", "quote": "The raw data and annotation files of GSE105149 and GSE58331 were downloaded from the GEO database."}, {"asset": "source:pmid:33613444", "locator": "sections[3] \"Characteristics of the Microarray Data Sets\" paragraph 2", "quote": "GSE105149 was the microarray data of various lacrimal gland tissues, including sarcoidosis, granulomatosis with polyangiitis, thyroid eye disease, nonspecific orbital inflammation and healthy controls (16)."}], "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:33613444"], "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:GSE105149"], "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:GSE105149"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33613444", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2020.571151", "sha256": "sha256:ca7b09de9446e37a6a31ce6d6abb63a501d797d43ccaf33123d324996d352f3a", "bytes": 37460, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2020.571151", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7888479", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE105149", "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=GSE105149", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE105149", "version": null, "note": "The raw data and annotation files of GSE105149 and GSE58331 were downloaded from the GEO database. 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