Identification of feature genes and pathways for Alzheimer's disease via WGCNA and LASSO regression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36213445", "kind": "science-record", "revision": 4, "content_hash": "sha256:c2b595d9705661cf42c38268ff6f7474582574254b79f3663a2c1ec4a799e0f1", "created_at": "2026-11-01T18:15:33Z", "updated_at": "2026-11-01T22:07:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of feature genes and pathways for Alzheimer's disease via WGCNA and LASSO regression.", "doi": "10.3389/fncom.2022.1001546", "pmid": "36213445", "authors": ["Hongyu Sun", "Jin Yang", "Xiaohui Li", "Yi Lyu", "Zhaomeng Xu", "Hui He", "Xiaomin Tong", "Tingyu Ji", "Shihan Ding", "Chaoli Zhou", "Pengyong Han", "Jinping Zheng"], "journal": "Frontiers in computational neuroscience", "year": 2022, "abstract": "While Alzheimer's disease (AD) can cause a severe economic burden, the specific pathogenesis involved is yet to be elucidated. To identify feature genes associated with AD, we downloaded data from three GEO databases: GSE122063, GSE15222, and GSE138260. In the filtering, we used AD for search keywords, Homo sapiens for species selection, and established a sample size of > 20 for each data set, and each data set contains Including the normal group and AD group. The datasets GSE15222 and GSE138260 were combined as a training group to build a model, and GSE122063 was used as a test group to verify the model's accuracy. The genes with differential expression found in the combined datasets were used for analysis through Gene Ontology (GO) and The Kyoto Encyclopedia of Genes and Genome Pathways (KEGG). Then, AD-related module genes were identified using the combined dataset through a weighted gene co-expression network analysis (WGCNA). Both the differential and AD-related module genes were intersected to obtain AD key genes. These genes were first filtered through LASSO regression and then AD-related feature genes were obtained for subsequent immune-related analysis. A comprehensive analysis of three AD-related datasets in the GEO database revealed 111 common differential AD genes. In the GO analysis, the more prominent terms were cognition and learning or memory. The KEGG analysis showed that these differential genes were enriched not only in In the KEGG analysis, but also in three other pathways: neuroactive ligand-receptor interaction, cAMP signaling pathway, and Calcium signaling pathway. Three AD-related feature genes (SST, MLIP, HSPB3) were finally identified. The area under the ROC curve of these AD-related feature genes was greater than 0.7 in both the training and the test groups. Finally, an immune-related analysis of these genes was performed. The finding of AD-related feature genes (SST, MLIP, HSPB3) could help predict the onset and progression of the disease. Overall, our study may provide significant guidance for further exploration of potential biomarkers for the diagnosis and prediction of AD.", "claims": [{"id": "claim-method", "statement": "This analysis was performed using the R package “weighted gene co-expression network analysis” (WGCNA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36213445", "locator": "sections[6] \"2.4. Network construction and module identification for weighted gene co-expression network analysis (WGCNA)\" paragraph 2", "quote": "This analysis was performed using the R package “weighted gene co-expression network analysis” (WGCNA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36213445", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified three AD-related feature genes, SST, MLIP, and HSPB3.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36213445", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Three AD-related feature genes (SST, MLIP, HSPB3) were finally identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified three AD-related feature genes, SST, MLIP, and HSPB3.", "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:36213445"], "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. 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