Screening of mRNA markers in early bovine tuberculosis blood samples.

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How to control bTB is an important issue in the current global livestock economy. In this study, the original transcriptome sequences related to this study were obtained from the dataset GSE192537 by searching the Gene Expression Omnibus (GEO) database. Our differential gene analysis showed that there were obvious biological activities related to immune activation and immune regulation in the early stage of bTB. Immune-related biological processes were more active in the early stage of bTB than in the late. There were obvious immune activation and immune cell recruitment in the early stage of bTB. Regulations in immune receptors are associated with pathophysiological processes of the early stage of bTB. A gene module consisting of 236 genes significantly related to the early stage of bTB was obtained by weighted gene co-expression network analysis, and 18 hub genes were further identified as potential biomarkers or therapeutic targets. Finally, by random forest algorithm and logistic regression modeling, FCRL1 was identified as a representative mRNA marker in early bTB blood. FCRL1 has the potential to be a diagnostic biomarker in early bTB.", "claims": [{"id": "claim-method", "statement": "We set up the SFN network of WGCNA to search for gene sets highly associated with different stages of bTB progression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38645645", "locator": "sections[5] \"Analysis of WGCNA gene co-expression network\" paragraph 2", "quote": "We set up the SFN network of WGCNA to search for gene sets highly associated with different stages of bTB progression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/; GSE192537.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38645645", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/; GSE192537."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results showed that the diagnostic Model constructed with FCRL1 as a predictor had the best performance with an average AUC of 95%, while the diagnostic model constructed with two genes had the worst performance with an average AUC of 85%.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38645645", "locator": "sections[17] \"Establishment and verification of early diagnosis model of bovine tuberculosis\" paragraph 4", "quote": "The results showed that the diagnostic Model constructed with FCRL1 as a predictor had the best performance with an average AUC of 95%, while the diagnostic model constructed with two genes had the worst performance with an average AUC of 85%."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The results showed that the diagnostic Model constructed with FCRL1 as a predictor had the best performance with an average AUC of 95%, while the diagnostic model constructed with two genes had the worst performance with an average AUC of 85%.", "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:38645645"], "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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