(b) KEGG pathway annotation summarized the enriched pathways for the targets ascribed to catalytic activity. (c) Illustration of how the boundary of active site is defined using the multiplexed-TRAP data. The minimal Euclidean distances between the TRPs of the TRAP-identified targets that use the...
Initiatives to support chemogenomics, such as the NIH Chemical Genomics Center (http://www.ncats.nih.gov/research/reengineering/ncgc/ncgc.html) and databases, such as ChemMapper and KEGG (Kyoto Encyclopedia of Genes and Genomes) also facilitate chemical genetics research. Next, we discuss two ...
Pathway diagram designed using the modified optStoic procedure: (A) ED pathway, (B) a lower cost 1 ATP-generating pathway, (C) EMP pathway and (D) a lower cost 2 ATP-yielding pathway. The label beside each arrow represents the KEGG reaction ID and flux through each reaction. ATP and ...
To gain insight into the biological role of these PTMs, we performed bioinformatics clustering with DAVID (Huang da et al., 2009) and KEGG analysis. These results reveal enrichment for proteins associated with carbon metabolism and glycolysis (Figure 4B and Table S2). We thus mapped identified ...
a KEGG and GO pathway enrichment analysis of 937 upregulated DEP categorized by functional annotation. GSEA analysis revealed that 937 DEPs are significantly enriched in b energy metabolism-related pathways; c cytoskeleton-related pathways; P-values were adjusted for multiple testing (FDR). d The ...
Genes associated with glycolysis and VEGF signaling pathways were shortlisted from KEGG datasets. The subnetwork was generated by pathway commons analysis, with dotted lines representing known regulatory relationships, physical interactions, and expression correlations among the genes. Node size is ...
enriched gene expression signatures between CTL-differentiated WT and mPiC-deficient T cells. Down- and upregulated gene signatures in mPiC-deficient T cells are shown in blue and red, respectively.f,gGene set enrichment analysis (GSEA) of (f)oxidative phosphorylation(KEGG pathway) and (g)effec...
A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed to determine the significantly changed pathways in which the co-expressed mRNAs are involved [47]. Based on the criteria of an FDR < 0.05 and aP-value < 0.01, we identified 15 upregulated pathways and ...
The coordination of immunity across organs is fundamental to cancer development and progression. It is well known that the hostile metabolic microenvironment in the tumour is a major obstacle to effective anti-tumour immunity. However, whether metabolic
In KEGG, B cell, T cell, Th1/Th2 cell differentiation-related pathway et al. in cancer were downregulated (Fig. 3C). In GO, B cell-mediated immunity and immunoglobulin-mediated immune response et al. were also downregulated (Fig. 3D). The above functional analyses suggested that B cells ...