Fig. 2 Signature of trait exaggeration among sex-biased genes. a–c Comparison of gene expression (log2 TPM + 1) in male and female legs. Dots highlighted in purple and blue represent genes with significant difference in expression in females and males respectively. Insets indicate the nu...
Fig. 1. The Y/X expression ratio level in male individuals of rhesus macaques, Tibetan macaques, and humans. The Y/X expression ratio was estimated as (Y-homolog TPM + 0.5)/(X-homolog TPM + 0.5) in individuals. We deleted the TPM of both Y homolog and X homolog less than one. Fur...
Expression abundance was calculated as log2(TPM + 1). The middle bar of all box plots corresponds to the median; the upper and lower bounds correspond to the third and first quartiles. The whiskers correspond to the upper and lower bounds 1.5 times the IQR. c, Expression correlation ...
A log2 expression cut-off of 1 TPM on average for each gene and variance of at least 1 were used to ensure enough information for co-expression analyses. Gene co-expression values were calculated using log2 TPM values for selected genes using WGCNA9 (v1.70-3) with the exponent equal to...
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[65]) implementation. In particular, the intersection of genes between batches was used. The cells were filtered to a minimum of 10 genes per cell and a minimum of 3 cells per gene. Library size normalization was performed to a value of 20000 with subsequent log-transformation. As model ...
Gene expression was quantied as transcripts per million (TPM) and log2-transformed (Goldman et al., 2020). A gene expression level is presented as low/medium/high depending on the expression level of a such gene in patients of the reference cohort. Low = < 17%; Medium = 17%-83%; ...
Additionally, a number of genes involved in the regulation of muscle contraction (Anxa6, Atp1a1, Gucy1a3, Myl9, Tpm1 and Tpm3) were found in this cluster and are possibly expressed by contractile peritubular myoid cells. Cluster B, which might correspond to somatic genes undergoing down ...
Principle Component values were generated using the R function prcomp() using all genes and visualized with R package ggplot2. DQ samples For a gene to be discordant, its expression in at least one data set should be more than 32 TPM (i.e. log2 (TPM+0.001) more than 5) and the log...
Scale represents median-centered counts (TPM). Full size image Next, we performed RNA sequencing to determine the genes and pathways that are disrupted in TREM2 KO human microglia. Two independent sets of TREM2 isogenic microglia generated from two distinct patients were sequenced to account for ...