Altered Genes and Biological Functions in Response to Severe Burns.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34124262", "kind": "science-record", "revision": 8, "content_hash": "sha256:425fcb2c99eb6852a720905495235dfec9e55bd647f244c156fef6cf9e2b51ff", "created_at": "2026-11-01T15:41:38Z", "updated_at": "2026-11-01T22:46:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Altered Genes and Biological Functions in Response to Severe Burns.", "doi": "10.1155/2021/8836243", "pmid": "34124262", "authors": ["Xinheng Liu", "Yongxian Rong", "Donglin Huang", "Zhijie Liang", "Xiaolin Yi", "Fangxiao Wu", "Dandan Zhu", "Steven Mo", "Wenhai Nong", "Hongmian Li"], "journal": "BioMed research international", "year": 2021, "abstract": "Severe burns are acute wounds caused by local heat exposure, resulting in life-threatening systemic effects and poor survival. However, the specific molecular mechanisms remain unclear. First, we downloaded gene expression data related to severe burns from the GEO database (GSE19743, GSE37069, and GSE77791). Then, a gene expression analysis was performed to identify differentially expressed genes (DEGs) and construct protein-protein interaction (PPI) network. The molecular mechanism was identified by enrichment analysis and Gene Set Enrichment Analysis. In addition, STEM software was used to screen for genes persistently expressed during response to severe burns, and receiver operating characteristic (ROC) curve was used to identify key DEGs. A total of 2631 upregulated and 3451 downregulated DEGs were identified. PPI network analysis clustered these DEGs into 13 modules. Importantly, module genes mostly related with immune responses and metabolism. In addition, we identified genes persistently altered during the response to severe burns corresponding to survival and death status. Among the genes with high area under the ROC curve in the PPI network gene, CCL5 and LCK were identified as key DEGs, which may affect the prognosis of burn patients. Gene set variation analysis showed that the immune response was inhibited and several types of immune cells were decreased, while the metabolic response was enhanced. The results showed that persistent gene expression changes occur in response to severe burns, which may underlie chronic alterations in physiological pathways. Identifying the key altered genes may reveal potential therapeutic targets for mitigating the effects of severe burns.", "claims": [{"id": "claim-method", "statement": "For burn patients and healthy subjects, the mRNA levels of DEGs were identified using the limma package [17].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34124262", "locator": "sections[4] \"2.2. DEG Analysis\" paragraph 2", "quote": "For burn patients and healthy subjects, the mRNA levels of DEGs were identified using the limma package [17]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The research data used to support the findings of this study are included within the supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34124262", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The research data used to support the findings of this study are included within the supplementary information files."}], "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:34124262"], "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:GSE19743"], "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:GSE19743"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34124262", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/8836243", "sha256": "sha256:7325fcd4c0ecd64f36bc0a03739b85b96129ddb61367cc4e611dc3a0d7520cdc", "bytes": 36447, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/8836243", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8168476", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19743", "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=GSE19743", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19743", "version": null, "note": "The research data used to support the findings of this study are included within the supplementary information files.", "structure": 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