Function to compute signature scores as linear combination of gene expressionsBenjamin HaibeKains
UCell 计算单细胞gene signature score 在做单细胞转录组数据分析时,我们经常遇到特定(通路/功能)基因集合的表达活性分析,目前比较常用的是GSVA以及Seurat软件包的AddModuleScore[1]函数。这里我们介绍一种新的方法UCell[2],它具有以下特点: UCell scores 对数据集的大小和异质性具有鲁棒性 UCell评分基于基因排序,因此...
A gene expression signature for high-risk multiple myeloma. Leukemia. (2012). , 26(11), 2406-13.Kuiper R, Broyl A, de Knegt Y, van Vliet MH, van Beers EH, van der Holt B, el Jarari L, Mulligan G, Gregory W, Morgan G, Goldschmidt H, Lokhorst HM, van Duin M, Sonneveld P ...
we first performed univariate Cox regression using the weighted Cam_121 expression score (see “Methods” section “Survival analyses”) as a predictor. We found that the Cam_121 signature significantly associated with both OS (hazard ratio (HR) = 1.64 (95% CI 1.30–2.07),p = 3.5...
When the combination of active genes is unique for a specific biological phenotype, this group of genes is known as “gene signature”. Finding this group of genes, whose expression pattern is unique to the studied condition, is one of the primary objectives in most gene expression profiling st...
Yes, the module score represents relative expression. If gene A is highly expressed across all cells, the module scores assess whether a given cell expresses gene A more often than other highly expressed genes. Therefore, if the module score is high, it indicates these genes are expressed. If...
These results support our conclusion that matrisome gene expression can serve as a key signature to determine individual cell types, as well as cell states. Intriguingly, using a comparative evolutionary approach, i.e., by correlating transcriptional pseudobulk signatures from both chicken and mouse,...
Using the EXALT online program we performed an analysis using the human cancer signature database to survey the co-expression profile for these two functionally discordant genes. The returned signatures were ranked by the sum of Q scores for the subject signature triplets from highest (top) to ...
(f) Fraction of total signature of each cell type present in the cortex, medulla, and pelvis in the adult human kidney (Ricardo et al.). Figure S3. Energy metabolism features of the renal cortex and medulla. Heatmaps displaying the expression levels of (a) OXPHOS-related genes and (b)...
Indexing gene expression data for comparing gene signatures includes assigning one of a plurality of fold change-based grading scores to each of a number of genes in a probe gene si