Function to compute signature scores as linear combination of gene expressionsBenjamin HaibeKains
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...
Since the score of gene set is unitless and reflects the likeliness of the gene set being more expressed that expected, it cannot give any information on the level of expression of the gene set, can it?If so, would it be an other way of assessing the level of co-expression of the spe...
(in this case, a neural network) that measures the probability of a gene expression signature corresponding to a molecular representation. The λ andαterms are regularization parameters, where the former one balances the influence of the gradient penalty term into the discriminator loss. Similarly,...
读文献--综述:Comparison and evaluation of pathway-leel aggregation methods of gene expression data Introduction Background 得到数据的功能性的理解集中于基因集的功能,比如pathways而不是单个基因.现在pathway-level的分析主要是ORA和GSEA,另外的方法也在探索.该方法首先在pathway层面整合基因表达数据,将原始数据转化...
The prognostic performance of each signature was evaluated via a meta-analysis of 1927 early stage NSCLC patients collected from 15 studies using three evaluation metrics (hazard ratios, concordance scores, and time-dependent receiver-operating characteristic curves). The performance of each signature ...
In a multivariable Cox model performed in the CALGB 40601 trial, the immunoglobulin G signature, but not tumor-infiltrating lymphocytes, was independently associated with event-free survival. Meaning Findings suggest that when both tumor-infiltrating lymphocytes and gene expression are available, the ...
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 ...
[1]. The score is scaled from −1 to +1, with negative scores indicating BRAFV600E-like signature and positive scores indicating RAS-like expression. The development of BRS has introduced the ability to assess whether the gene expression of a non-mutant thyroid neoplasm is similar to that...
We were not able to assess the AMR gene signature because only 2 samples showed signs of AMR. As previously described11, we calculated the sum of Z-scores for these 6 genes and compared R and NR samples. The results presented in Fig. 4A show that the sum of Z-scores using Nanostring...