Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files

Kancherla, Jayaram; Yang, Yifan; Chae, Hyeyun; Bravo, Héctor Corrada

doi:10.1101/865295

Cited by 1 publication

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References 33 publications

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“…org/ gsea/ index. jsp) of based on "clusterProfiler" and "AnnotationHub" algorithms [24,25]. Here, the algorithmic parameters of the number of genes in the minimum gene set is 10, as well as 500 in the largest gene set.…”

Section: Gene Set Enrichment Analysis and Gene Set Variation Analysismentioning

confidence: 99%

A circular network of purine metabolism as coregulators of dilated cardiomyopathy

et al. 2022

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Background The crosstalk of purine biosynthesis and metabolism exists to balance the cell energy production, proliferation, survival and cytoplasmic environment stability, but disorganized mechanics of with respect to developing heart failure (HF) is currently unknown. Methods We conducted a multi-omics wide analysis, including microarray-based transcriptomes, and full spectrum metabolomics with respect to chronic HF. Based on expression profiling by array, we applied a bioinformatics platform of quantifiable metabolic pathway changes based on gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), Shapley Additive Explanations (SHAP), and Xtreme Gradient Boosting (XGBoost) algorithms to comprehensively analyze the dynamic changes of metabolic pathways and circular network in the HF development. Additionally, left ventricular tissue from patients undergoing myocardial biopsy and transplantation were collected to perform the protein and full spectrum metabolic mass spectrometry. Results Systematic bioinformatics analysis showed the purine metabolism reprogramming was significantly detected in dilated cardiomyopathy. In addition, this result was also demonstrated in metabolomic mass spectrometry. And the differentially expressed metabolites analysis showing the guanine, urea, and xanthine were significantly detected. Hub markers, includes IMPDH1, ENTPD2, AK7, AK2, and CANT1, also significantly identified based on XGBoost, SHAP model and PPI network. Conclusion The crosstalk in the reactions involved in purine metabolism may involving in DCM metabolism reprogramming, and as coregulators of development of HF, which may identify as potential therapeutic targets. And the markers of IMPDH1, ENTPD2, AK7, AK2, and CANT1, and metabolites involved in purine metabolism shown an important role.

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Section: Gene Set Enrichment Analysis and Gene Set Variation Analysismentioning

confidence: 99%

A circular network of purine metabolism as coregulators of dilated cardiomyopathy

et al. 2022

View full text Add to dashboard Cite

show abstract

Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files

Cited by 1 publication

References 33 publications

A circular network of purine metabolism as coregulators of dilated cardiomyopathy

A circular network of purine metabolism as coregulators of dilated cardiomyopathy

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