Methods We propose a new approach based on enrichment analysis at the level of samples (sample-level enrichment analysis - SLEA) in expression profiling datasets. Without using a priori phenotypic information about samples, SLEA calculates an enrichment score per sample per gene set using z-test....
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA) - broadinstitute/ssGSEA2.0
Additionally, we performed single-sample Gene Set Enrichment Analysis (ssGSEA) between different subgroups using the R package ‘GSEABase’ [24]. CIBERSORT was to employed analyze immune cell infiltration. We used the Wilcoxon test for comparisons between two groups, and the Kruskal-Wallis test ...
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2E). In addition, Gene Set Enrichment Analysis (GSEA) of proteins, phosphorylation sites, and acetylation sites shows that gene sets associated with basal and luminal breast cancer subtypes are appropriately regulated in data acquired with and without initial enrichment of ubiquitylated peptides using ...
In scenario IV, we set the probability of each cell belonging to either of the three cell types in each spatial domain to be equal (1/3). Therefore, scenario I represents one extreme case where one cell type completely dominates a spatial domain; scenario IV represents the other extreme ...
The U.S. Department of Energy (DOE) has already set a target for H2 storage, namely, a gravimetric capacity of 5.5 wt% and a volumetric capacity of 0.04 kg•L − 1 in the temperature range from 233 to 333 K by 2020.209 For hydrogen storage, a stable structure with ultra-large ...
Gene Set Enrichment Analysis GO: Gene Ontology MSigDB: Molecular Signatures Database AUC: Area under the curve TPM: Transcripts per million DEMRGs: Differential Expressed Metabolism-Related Genes SVM-RFE: Support vector machine recursive feature elimination IHC: Immunohistochemistry HPA: Human...
specificity (KR not P) and allowing up to two missed cleavage sites. Cysteine carbamidomethylation was set as a fixed modification andmethionineoxidationas well as N-terminalacetylationof proteins as variable modifications. For phosphopeptide analysis phosphorylation (S,T,Y) was added as an additional...
Pathway analysis Pathway analysis was use to extract biological information within relevant networks of metabolic pathways. Pathway analysis integrates metabolite set enrichment analysis and pathway topology analysis11. Using quantile normalization and autoscaling as data pretreatment, the pathway enrichment and...