Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers.

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Materials and methods: GSE158767 dataset were used to process WGCNA analysis, differential gene analysis, Gene ontology and KEGG analysis, protein-protein network analysis and hub genes analysis. Based on our previous study, the intersect between WGCNA and differential gene analysis could be used as candidate biomarkers. Then, the enzyme-linked immunosorbent assay was used to validate candidate biomarkers, and receiver operating characteristic was used to assess diagnose ability of candidate biomarkers. Results: A total of 412 differential genes were screened. And we obtained 105 overlapping genes between DEGs and WGCNA. GO and KEGG analysis showed that most of the differential genes were significantly enriched in innate immunity. A total of 15 hub genes were screened, and four of them were verified by Enzyme-linked immunosorbent assay. CCL5 performed well in distinguishing the healthy group from the TB group (AUC = 0.723). And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811). Conclusion: CCL19, C1Qb, CCL5 and HLA-DMB may play important role in tuberculosis, which indicated four genes may become effective biomarkers and could be conveniently used to facilitate the individual tuberculosis diagnosis in Chinese people.", "claims": [{"id": "claim-method", "statement": "Student’s t-test was used to compare the differences between the two groups, and p < 0.05 was considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35345666", "locator": "sections[8] \"Verification of the Candidate Biomarkers\" paragraph 2", "quote": "Student’s t-test was used to compare the differences between the two groups, and p < 0.05 was considered statistically significant."}], "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:35345666", "locator": "sections[17] \"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": "And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811).", "kind": "quantitative", "target": {"value": 0.811, "unit": "auc", "tolerance": null, "source": "And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811)."}, "evidence": [{"asset": "source:pmid:35345666", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811).", "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:35345666"], "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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Then, the enzyme-linked immunosorbent assay was used to validate candidate biomarkers, a", "screened, and four of them were verified by Enzyme-linked immunosorbent assay. CCL5 performed well in distinguishing the h", "nd Methods Experimental Verification We used ELISA to validate the four candidate biomarkers sc", "C, AUC = 0.788; TB vs ORD, AUC = 0.880). The ELISA verification of four biomarkers. HC, healthy"], "order_basis": "paper_text_order:557", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["logistic regression"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}