Identification and Validation of Novel Genes in Anaplastic Thyroid Carcinoma via Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33116838", "kind": "science-record", "revision": 8, "content_hash": "sha256:a1d4ef41e73da87c0cdc8b37876c9b941e01ecd917e032f17f81190b113a13c6", "created_at": "2026-11-01T15:41:14Z", "updated_at": "2026-11-01T22:02:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of Novel Genes in Anaplastic Thyroid Carcinoma via Bioinformatics Analysis.", "doi": "10.2147/CMAR.S250792", "pmid": "33116838", "authors": ["Shengnan Wang", "Jing Wu", "Congcong Guo", "Hongxia Shang", "Jinming Yao", "Lin Liao", "Jianjun Dong"], "journal": "Cancer management and research", "year": 2020, "abstract": "PURPOSE: The conventional interventions of anaplastic thyroid carcinoma (ATC) patients are mainly through surgery, chemotherapy, and radiotherapy; however, it is hardly to improve survival rate. We aimed to investigate the differential expressed genes (DEGs) between ATC and normal thyroid gland through bioinformatics analysis of the microarray datasets and find new potential therapeutic targets for ATC.\nMETHODS: Microarray datasets GSE9115, GSE29265, GSE33630, GSE53072, and GSE65144 were downloaded from Gene Expression Omnibus (GEO) database. Compared with the normal tissue, GEO2R was conducted to screen the DEGs in each chip under the condition of |log FC| > l, adjusted P-values (adj. P) < 0.05. The Retrieval of Interacting Genes (STRING) database was used to calculate PPI networks of DEGs with a combined score >0.4 as the cut-off criteria. The hub genes in the PPI network were visualized and selected according to screening conditions in Cytoscape software. In addition, the novel genes in ATC were screened for survival analysis using Kaplan-Meier plotter from those hub genes and validated by RT-qPCR.\nRESULTS: A total of 284 overlapping DEGs were obtained, including 121 upregulated and 161 downregulated DEGs. A total of 232 DEGs were selected by STRING database. The 50 hub genes in the PPI network were chosen according to three screening conditions. In addition, the Kaplan-Meier plotter database confirmed that high expressions of ANLN, CENPF, KIF2C, TPX2, and NDC80 were negatively correlated with poor overall survival of ATC patients. Finally, RT-qPCR experiments showed that KIF2C and CENPF were significantly upregulated in ARO cells and CAL-62 cells when compared to Nthy-ori 3-1 cells, TPX2 was upregulated only in CAL-62 cells, while ANLN and NDC80 were obviously decreased in ARO cells and CAL-62 cells.\nCONCLUSION: Our study suggested that CENPF, KIF2C, and TPX2 might play a significant role in the development of ATC, which could be further explored as potential biomarkers for the treatment of ATC.", "claims": [{"id": "claim-method", "statement": "Student’s t-test was used to analyze statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33116838", "locator": "sections[10] \"Statistical Analysis\" paragraph 2", "quote": "Student’s t-test was used to analyze statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE9115 dataset included five ATC tissues and four normal thyroid tissues (noncancerous samples, normal thyroid specimens).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33116838", "locator": "sections[3] \"ATC Dataset Preprocessing\" paragraph 3", "quote": "The GSE9115 dataset included five ATC tissues and four normal thyroid tissues (noncancerous samples, normal thyroid specimens)."}], "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:33116838"], "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:GSE29265"], "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:GSE29265"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33116838", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S250792", "sha256": 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"Forward 5’-GTCAGCCAATGCAGGGACAC-3’Reverse 5’- TGCCAGAGGCGAATATCAACAA-3’"], ["CENPF", "Forward 5’- CCCACTGAGTCTCGGCAAAG-3’Reverse 5’- GAGGATGGTGCCTGAATCTACTG-3’"], ["KIF2C", "Forward 5’- AGCTGACACAGGTGCTGAGG-3’Reverse 5’- TGTCTGCATATCTCAGGGGTGTTTA-3’"], ["TPX2", "Forward 5’- GCTCTGAAGGCACAGACTTGGA-3’Reverse 5’- AGAGATGACGGTGTTTGGACGA-3’"], ["NDC80", "Forward 5’- AACCAAGGACCTGGAAGCTGAAC-3’Reverse 5’- TTTGGAATTCTCAGCACCTTTAGGA-3’"], ["GAPDH", "Forward 5’-CAGAACATCATCCCTGCCTCTAC-3’Reverse 5’-TTGAAGTCAGAGGAGACCACCTG-3’"]], "row_count": 7, "column_count": 2, "numeric_cells": 7, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t0001"}}], "gaps": ["asset:data:geo:GSE29265 not downloaded", "asset:data:geo:GSE29265 licence not read", "asset:data:geo:GSE33630 not downloaded", "asset:data:geo:GSE33630 licence not read", "asset:data:geo:GSE53072 not downloaded", "asset:data:geo:GSE53072 licence not read", "asset:data:geo:GSE65144 not downloaded", "asset:data:geo:GSE65144 licence not read", 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METHODS: Microarray datasets GSE9115, GSE29265, GSE33630, GSE530"], "order_basis": "paper_text_order:396", "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": ["lotter from those hub genes and validated by RT-qPCR. RESULTS: A total of 284 overlapping DEGs we", "r overall survival of ATC patients. Finally, RT-qPCR experiments showed that KIF2C and CENPF were", "ter from those hub genes and validated by RT-qPCR. RESULTS: A total of 284 overlapping DEGs we", "verall survival of ATC patients. Finally, RT-qPCR experiments showed that KIF2C and CENPF were"], "order_basis": "paper_text_order:1171", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["hyroglobulin (TG) expression was detected by immunofluorescence in ARO cells. TG is a specific marker protei"], "order_basis": "paper_text_order:4706", "id": "assay:3"}, {"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": ["handong First Medical University. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (G"], "order_basis": "paper_text_order:5247", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}