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pmid:30115125
Identification of target genes in cardiomyopathy with fibrosis and cardiac remodeling.
Jianquan Zhao · Tiewei Lv · Junjun Quan · Weian Zhao · Jing Song · Zhuolin Li · Han Lei · Wei Huang · Longke Ran
Journal of biomedical science · 2018 doi:10.1186/s12929-018-0459-8
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Complete file
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Differential expression of genes (DEGS) between the two groups of total 14 cardiomyopathy patients and 10 healthy controls were subsequently identified by limma package of R. Database for Annotation, Visualization, and Integrated Discovery (DAVID Tool), which is an analysis of enriched biological processes. Search Tool for the Retrieval Interacting Genes (STRING) was used as well for the analysis of protein-protein interaction network (PPI). Prediction of the potential drugs was suggested based on the preliminarily identified genes using Connectivity Map (CMap).\nRESULTS: Eighty-nine DEGs were identified (57 up-regulated and 32 down-regulated). The most enrichment Gene Ontology (GO) terms (P < 0.05) contain genes involved in extracellular matrix (ECM) and biological adhesion signal pathways (P < 0.05, ES > 1.5) such as ECM-receptors, focal adhesion and transforming growth factor beta (TGF-β), etc. Fifty-one differentially expressed genes were found to encode interacting proteins. Eleven key genes along with related transcription factors were identified including CTGF, POSTN, CORIN, FIGF, etc. CONCLUSION: Bioinformatics-based analyses reveal the targeted genes probably associated with cardiomyopathy, which provide clues for pharmacological therapies aiming at the targets.", "claims": [{"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30115125", "locator": "sections[18] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using limma in R with P < 0.05 and |log2(fold change)| ≥ 1 on the GEO GSE3585 and GSE42955 datasets, the study identified 89 differentially expressed genes, comprising 57 up-regulated and 32 down-regulated genes.", "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:30115125"], "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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