Identification of differentially expressed genes and signaling pathways in papillary thyroid cancer: a study based on integrated microarray and bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33708546", "kind": "science-record", "revision": 4, "content_hash": "sha256:443c63a586f1c83a7e72370baf02ba4f764187bf391075b5ae178ad0ac4ae7d3", "created_at": "2026-11-01T17:34:53Z", "updated_at": "2026-11-01T22:03:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes and signaling pathways in papillary thyroid cancer: a study based on integrated microarray and bioinformatics analysis.", "doi": "10.21037/gs-20-673", "pmid": "33708546", "authors": ["Tuanqi Sun", "Qing Guan", "Yunjun Wang", "Kai Qian", "Wenyu Sun", "Qinghai Ji", "Yi Wu", "Kai Guo", "Jun Xiang"], "journal": "Gland surgery", "year": 2021, "abstract": "BACKGROUND: The techniques of DNA microarray and bioinformatic analysis have exhibited efficiency in identifying dysregulated gene expression in human cancers. In this study, we used integrated bioinformatics analysis to improve our understanding of the pathogenesis of papillary thyroid cancer (PTC).\nMETHODS: In this study, we integrated four Gene Expression Omnibus (GEO) datasets, GSE33630, GSE35570, GSE60542 and GSE29265, including 136 normal samples and 157 PTC specimens. The contents of the four datasets are based on GPL570, an Affymetrix Human Genome U133 Plus 2.0 array. Gene ontology (GO) analysis was used to identify characteristic the biological attributes of differentially expressed genes (DEGs) between PTC and normal samples. GO annotation was performed on the DEGs obtained, and the process relied on the DAVID online tool. Kyoto Encyclopedia of Genes and Genomes (KEGG) approach enrichment analyses were adopted to obtain the basic functions of the DEGs. The KOBAS online analysis database was used to complete DEG KEGG pathway comparison and analysis. The search tool (STRING) database was mainly used to search for interacting genes and complete the construction of protein-protein interaction (PPI) networks.\nRESULTS: Five hundred-ninety DEGs were consistently expressed in the four datasets; 327 of them were upregulated, while 263 were downregulated. Ten DEGs, including five upregulated (ENTPD1, THRSP, KLK10, ADAMTS9, MIR31HG) and five downregulated (SCARA5, EPHB1, CHRDL1, LOC440934, FOXP2) genes, were randomly selected for q-PCR in our own tissue samples to validate the integrated data. The most highly enriched GO terms were extracellular exosome (GO:0070062), cell adhesion (GO:0070062), positive regulation of gene expression (GO:0010628), and extracellular matrix (ECM) organization (GO:0030198). KEGG pathway analysis was performed, and it was found that abnormally expressed genes effectively participated in pathways such as tyrosine metabolism, complement and coagulation cascades, cell adhesion molecules (CAMs), transcriptional misregulation and ECM-receptor interaction pathways.\nCONCLUSIONS: Five hundred-ninety DEGs were identified in PTC by integrated microarray analysis. The GO and KEGG analyses presented here suggest that the DEGs were enriched in extracellular exosome, tyrosine metabolism, CAMs, complement and coagulation cascades, transcriptional misregulation and ECM-receptor interaction pathways. Functional studies of PTC should focus on these pathways.", "claims": [{"id": "claim-data-access", "statement": "In this study, we integrated four Gene Expression Omnibus (GEO) datasets, GSE33630, GSE35570, GSE60542 and GSE29265, including 136 normal samples and 157 PTC specimens. The contents of the four datasets are based on GPL570, an Affymetrix Human Genome U133 Plus 2.0 array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33708546", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In this study, we integrated four Gene Expression Omnibus (GEO) datasets, GSE33630, GSE35570, GSE60542 and GSE29265, including 136 normal samples and 157 PTC specimens. The contents of the four datasets are based on GPL570, an Affymetrix Human Genome U133 Plus 2.0 array."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Five hundred-ninety DEGs were identified in PTC by integrated microarray analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33708546", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Five hundred-ninety DEGs were identified in PTC by integrated microarray analysis."}, {"asset": "source:pmid:33708546", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The GO and KEGG analyses presented here suggest that the DEGs were enriched in extracellular exosome, tyrosine metabolism, CAMs, complement and coagulation cascades, transcriptional misregulation and ECM-receptor interaction pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Five hundred-ninety DEGs were identified in PTC by integrated microarray analysis.", "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:33708546"], "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:33708546", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/gs-20-673", "sha256": "sha256:3f9a8326a7dd2b2e5e7e5adfd8208ba31efd2f05ec53240b9c316ceae30fd39e", "bytes": 2482, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/gs-20-673", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7944059", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29265", "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=GSE29265", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29265", "version": null, "note": "In this study, we integrated four Gene Expression Omnibus (GEO) datasets, GSE33630, GSE35570, GSE60542 and GSE29265, including 136 normal samples and 157 PTC specimens. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE33630", "GSE35570", "GSE60542", "GSE29265"], "resolved_accessions": ["GSE33630", "GSE35570", "GSE60542", "GSE29265"], "statements": ["In this study, we integrated four Gene Expression Omnibus (GEO) datasets, GSE33630, GSE35570, GSE60542 and GSE29265, including 136 normal samples and 157 PTC specimens. The contents of the four datasets are based on GPL570, an Affymetrix Human Genome U133 Plus 2.0 array."], "basis": "The paper names GSE33630, GSE35570, GSE60542, GSE29265 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33708546", "data:geo:GSE29265"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29265"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:01:33Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2150, "completion_tokens": 1353, "cached_tokens": 128}}, "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:33708546", "type": "paper", "label": "pmid:33708546"}, {"id": "source:pmid:33708546", "type": "manuscript", "label": "PMID 33708546 full text"}, {"id": "data:geo:GSE29265", "type": "dataset", "label": "GEO GSE29265"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33708546", "type": "paper", "label": "pmid:33708546"}, {"id": "source:pmid:33708546", "type": "manuscript", "label": "PMID 33708546 full text"}, {"id": "data:geo:GSE29265", "type": "dataset", "label": "GEO GSE29265"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33708546", "type": "extraction", "used": ["source:pmid:33708546"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29265", "type": "accession_resolution", "used": ["data:geo:GSE29265"], "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:33708546", "parent_hash": "sha256:54a2a169d723874f6a88046d214d8b6fa9b17d084ab3c2e8f0e510aced843334", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE29265 licence not read", "asset:data:geo:GSE29265 not downloaded", "asset:data:geo:GSE33630 licence not read", "asset:data:geo:GSE33630 not downloaded", "asset:data:geo:GSE35570 licence not read", "asset:data:geo:GSE35570 not downloaded", "asset:data:geo:GSE60542 licence not read", "asset:data:geo:GSE60542 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["thyroid cancer: a study based on integrated microarray and bioinformatics analysis.", "BACKGROUND: The techniques of DNA microarray and bioinformatic analysis have exhibited ef", "ty DEGs were identified in PTC by integrated microarray analysis. The GO and KEGG analyses presented", "of the four datasets are based on GPL570, an Affymetrix Human Genome U133 Plus 2.0 array. Gene ontol"], "order_basis": "paper_text_order:85", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}