Cells constantly face environmental challenges and deal with them by changing their gene expression patterns. They make decisions regarding which genes to express and which genes not to express based on intra-cellular and environmental cues. These decisions are often made by regulating the process of...
As stated in the Results, no significant DE genes are found, indicating that lineage information is not reflected in the gene expression profiles under different clones. Then, for the same Fore/Midbrain cells under subtree 9, 10, and 12, we compute their linear dimensionality reduction using ...
Gaussian kernel density estimation to compute density of cells from various conditions in the UMAP embedding was performed using Scanpy’s tl.embedding_density. Pre-ranked gene set enrichment analysis (GSEA) was implemented in fgsea (v1.24), using the Wald statistic as the gene rank metric. ...
Visual-based inspection of read coverage from RNA-sequencing enables the assessment of bioinformatics methods used to compute gene and isoform expression levels [29], [31], [83], [84]. Genome browsers such as Integrative Genomics Viewer (IGV) and University of California Santa Cruz (UCSC) Genom...
To remove cells of poor quality, we used scater [103] to compute QC metrics. For each barcode, we assessed the total UMI counts, total number of genes detected, and the proportion of counts mapping to mitochondrial genes (Additional file 1: Fig. S2A). We removed any barcodes that deviat...
We introduce an algorithm for the optimal control of stochastic nonlinear systems subject to temporal logic constraints on their behavior. We compute direc... MB Horowitz,EM Wolff,RM Murray - IEEE 被引量: 15发表: 2014年 A versatile cost-effective method for the analysis of fresh frozen tissue...
Patterns of gene expression were assessed by unsupervised hierarchical clustering using Euclidean distance and Ward as distance and clustering methods, respectively. The Bayes moderated t-statistics was used to compute differentially expressed genes (DEG); a false discovery rate (FDR) below 0.05 was ...
we can compute the total number of reads mapping to each repetitive element subfamily (Additional file 1:Figure S1A), which we refer to astotal counts. Second, we can compute the total number of reads mapping exclusively to a single repetitive element subfamily. This methodology is similar to...
This is especially true for liposome-based SCs operating by gene expression. Autopoietic SCs (composed of DNA, RNA, ribosomes, enzymes, lipids, . . . ) require the in situ production of their components. In turn, these production processes require enzymes (and ribosomes) to function, and ...
< 0.05 between LS and their corresponding sibling NPC controls (data not shown). The overlap of the DEGs from the three families, however, was relatively small, indicating a high level of gene expression variation in these NPC samples. Additional LS/control sets, analysis of multiple clones fro...