Finally, to correct for the number of genes tested and identify significant eGenes, we performed a q-value correction62 for the top associated SNP–gene pair, setting a q-value threshold of 0.1. Analysis of eQTL sharing across cell types To assess the sharing between eQTLs, we performed a ...
The scatter plot shows expression results for up to 219 genes in 51 samples as quantified by Nanostring on the FFPE sample and corresponding RNAlater preserved biopsy. Statistic shows the Spearman rank correlation value. Full size image Figure 2 Representation by heat map of Z-score values ...
bResults of comparing BRCA1 and NRF2 gene targets (“NFE2L2.V2” MSigDB gene set).aInteractive histogram showing the location of the NRF2-pathway genes (blue bars overlaid on histogram on left) within the correlation value distribution of BRCA1 with linked data table (right panel). ...
although the gene selection is done exclusively based on the training set. Figure9(b)depicts the Sammon's plot using the dormant genes. Comparing the Sammon's plot with the dominant genes, we find that although the dormant genes approximately reveal the class structures, these...
pis apvalue prior to FDR adjustment,padjis an FDR-adjustedpvalue,Ntestsis the number of correlation tests for which the FDR adjustment ofpvalues was made, andnis the sample size (the number of cell lines used in estimation or the number of pairs included in the correlation analysis).We ...
Another aesthetic feature of the subculture of Sakawa and the penchant for expensive material goods by Sakawa boys, is succinctly revealed in the following excerpt by a prominent member of a group when asked why some of them value expensive commodities: ...
(shown as dots) and summarized by the boxplots and the mean (dashed gray line) for different cut-offs on adjustedpvalue (x-axis). As controls for DEseq2, we used the whole training set of breast tissue. We also tested with a random subset of 5 controls and show the mean as the ...
Elements above the dotted line (q-value < 0.05 after multiple testing correction) are significantly enriched. (C) Repeatmasker alignment of two de novo POGZ binding motifs identified by MEME-CHIP analysis of POGZ C&R data. (D) Plot and Heatmap of ATAC-seq signal at instances of predicted ...
To compare SNP polymorphism levels in non-spidroin and spidroin loci, the value for four haploid individuals was applied when calculating θW for non-spidroin loci and the value for six haploid individuals was used for calculating θW in spidroin loci. The distribution of θW values for non-sp...
value for the black class is 0.61 while SNR (OVA) for the same class is 1.54. Note that, since we are using one-versus-all philosophy, a SNR value of 1.54 is expected to be much more significant than a GDI value of 0.61. The most significant difference between SNR (OVA) and GDI ...