Identification of key pathways, genes and immune cell infiltration in hypoxia of high-altitude acclimatization via meta-analysis and integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37035734", "kind": "science-record", "revision": 2, "content_hash": "sha256:d3cc7dcafcc83181d2605e597f63024abe25f5e6ccd56adc240bc4bc2b4af648", "created_at": "2026-11-01T19:01:41Z", "updated_at": "2026-11-01T21:30:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key pathways, genes and immune cell infiltration in hypoxia of high-altitude acclimatization via meta-analysis and integrated bioinformatics analysis.", "doi": "10.3389/fgene.2023.1055372", "pmid": "37035734", "authors": ["Qiong Li", "Zhichao Xu", "Fujin Fang", "Yan Shen", "Huan Lei", "Xiaobing Shen"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: For individuals acutely exposed to high-altitude regions, environmental hypobaric hypoxia induces several physiological or pathological responses, especially immune dysfunction. Therefore, hypoxia is a potentially life-threatening factor, which has closely related to high-altitude acclimatization. However, its specific molecular mechanism is still unclear. Methods: The four expression profiles about hypoxia and high altitude were downloaded from the Gene Expression Omnibus database in this study. Meta-analysis of GEO datasets was performed by NetworkAnalyst online tool. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene ontology (GO) enrichment analysis, and visualization were performed using R (version 4.1.3) software, respectively. The CIBERSORT analysis was conducted on GSE46480 to examine immune cell infiltration. In addition, we experimentally verified the bioinformatics analysis with qRT-PCR. Results: The meta-analysis identified 358 differentially expressed genes (DEGs), with 209 upregulated and 149 downregulated. DEGs were mostly enriched in biological processes and pathways associated with hypoxia acclimatization at high altitudes, according to both GO and KEGG enrichment analyses. ERH, VBP1, BINP3L, TOMM5, PSMA4, and POLR2K were identified by taking intersections of the DEGs between meta-analysis and GSE46480 and verified by qRT-PCR experiments, which were inextricably linked to hypoxia. Immune infiltration analysis showed significant differences in immune cells between samples at sea level and high altitudes. Conclusion: Identifying the DEGs and pathways will improve our understanding of immune function during high-altitude hypoxia at a molecular level. Targeting hypoxia-sensitive pathways in immune cells is interesting in treating high-altitude sickness. This study provides support for further research on high-altitude acclimatization.", "claims": [{"id": "claim-method", "statement": "As a result of the batch-effect adjustment, a random-effects model (REM) was used in Combining Effect Sizes for the meta-analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37035734", "locator": "sections[4] \"2.2 Data normalization, meta-analysis and identification of DEGs\" paragraph 3", "quote": "As a result of the batch-effect adjustment, a random-effects model (REM) was used in Combining Effect Sizes for the meta-analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. 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This data can be found here: https://www.ncbi.nlm.nih.gov/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The meta-analysis identified 358 differentially expressed genes, with 209 upregulated and 149 downregulated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37035734", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The meta-analysis identified 358 differentially expressed genes (DEGs), with 209 upregulated and 149 downregulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The meta-analysis identified 358 differentially expressed genes, with 209 upregulated and 149 downregulated.", "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:37035734"], "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:GSE116660"], "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:GSE116660"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37035734", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1055372", "sha256": "sha256:657d656ec71cdfc6ca0bd31c2e0745941fd0ec13f810e823836a0afdec7b1bc8", "bytes": 55602, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2023.1055372", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10080023", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116660", "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=GSE116660", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116660", "version": null, "note": "Publicly available datasets were analyzed in this study. 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