The impact of HBx protein on mitochondrial dynamics and associated signaling pathways strongly depends on the Hepatitis B virus genotype
Description
This dataset represents raw-data depicted in kinome analyses performed in the study (Figure 2). Kinases marked in blue represent deregulated kinases over the threshold of Mean Final Score >1.3. Mean kinase statistic refers to change in kinase activity in log2-space. SD kinase statistic refers to SD of kinase activity. For further information, please refer to the material and methods section of the study currently being under revision at Journal of Virology (refer to: JVI00424-24).
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For details, please check the publication indicated in the description. The materials and methods section addressing kinome profiling can be found as copy here: Transiently transfected cells were harvested 72 h post transfection by adding M-PER™ Mammalian Protein Extraction Reagent (Thermo Scientific, 78503) including Halt™ Protease Inhibitor Cocktail (Thermo Scientific, 87785) and Halt™ Phosphatase Inhibitor Cocktail (Thermo Scientific, 78420). The protein concentration was measured using Pierce™ BCA Protein Assay Kit (Thermo Scientific, 23225) and equal protein amount were used to detect phosphorylation status of target-peptides of distinct tyrosine- (PTK) or serine-threonine kinase (STK) of the lysate. STK and PTK PamChip microarrays were loaded and measured with respective reagents kits (PamGene International) using the PamStation®12 instrument. Phosphorylation sites of defined peptides, determined by fluorescent labelled antibody, were predicted and correlated to upstream kinase activities by using the BioNavigator software (v6.3.67), as described elsewhere [59]. The kinase final score is calculated by the specificity of the peptides corresponding to the kinases and the significance of the changed phosphorylations in the peptides. The kinase activity represents either up or downregulation of the respective kinase, compared to the control. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed with KEGG Orthology Based Annotation System (KOBAS, v3.0) database tool [60]. Gene list of predicted, statistically enriched kinome data, with a mean final score above 1.2 was applied to conduct pathway enrichment analysis by using the default module settings. Enriched terms with a p value above 0.05 were visualized in a bubble blot [61]. [59] Hurkmans DP, Verdegaal EME, Hogan SA, Wijn R de, Hovestad L, van den Heuvel DMA et al. Blood-based kinase activity profiling: a potential predictor of response to immune checkpoint inhibition in metastatic cancer. J Immunother Cancer 2020;8(2). https://doi.org/10.1136/jitc-2020-001607. [60] Bu D, Luo H, Huo P, Wang Z, Zhang S, He Z et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res 2021;49(W1):W317-W325. https://doi.org/10.1093/nar/gkab447. [61] Center for Bioinformatics Peking University & Institute of Computing Technology, Chinese Academy of Sciences. KOBAS-intelligence. [August 21, 2023]; Available from: http://kobas.cbi.pku.edu.cn/.