t1=as.data.frame(t1) t1$geneid=mcols(t2)[,1] # 如果觉得速度不够,就参考R语言实现并行计算 # http://www./956.html g_l = lapply(split(t1,t1$geneid),function(x){ # x=split(t1,t1$geneid)[[1]] head(x) tmp=apply(x,1,function(y){ y[2]:y[3] }) length(unique(unlist(tmp...
cBioPortal was utilized to assess TPM1-4gene alteration in HCC. TIMER2.0 was used for investigating the relevance of TPM1-4 to tumor-infiltrating immune cells in HCC. Additionally, we constructed a TPM1-4 prognostic model to explore the value of TPM1-4 for prognostic evaluation in HCC. ...
Upper Quartile FPKM The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the protein coding gene in the 75th percentile position is substituted for the sequencing quantity. This is thought to provide a more stable value than including the noisier genes at the extremes. TPM...
Upper Quartile FPKM The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the protein coding gene in the 75th percentile position is substituted for the sequencing quantity. This is thought to provide a more stable value than including the noisier genes at the extremes. TPM...
IV 双峰驼TPM2 与TPM3基因表达模式及其功能探究 关键词:双峰驼;原肌球蛋白2;原肌球蛋白3;肌纤维细胞;凋亡 V 甘肃农业大学2020届硕士学位论文 SUMMARY As an ancient and unique animal, Bactrian camel has inestimable research value. Bactrian camel belongs to the typical spermatozoa-induced platoon animal, ...
TPM stands for transcript per million, and the sum of all TPM values is the same in all samples, such that a TPM value represents a relative expression level that, in principle, should be comparable between samples [18]. $$TPM_{i} = \frac{{q_{i} /l_{i} }}{{\mathop \sum \no...
(exp1[i,])y<-as.numeric(exp1[j,])if(sum(exp1[i,])*sum(exp1[j,])!=0)#取出表达值都为0的行,如果要严格一点,想要把表达值出现0的行都去掉的话可以把求和函数sum()换成求积函数prod(x){gene_cor<-cor.test(x,y,alternative="two.sided",method="pearson")gene_p<-gene_cor$p.value...
gene_up=DEG[DEG$g=='UP','ENTREZID']gene_down=DEG[DEG$g=='DOWN','ENTREZID']}# 最简单的超几何分布检验###这里就拿KEGG数据库举例吧,拿自己判定好的上调基因集进行超几何分布检验,如下if(T){gene_downgene_upenrichKK<-enrichKEGG(gene=gene_up,organism='mmu',#universe = gene_all,pvalue...
ylab("-log10Pvalue") + geom_point(size=1,alpha=0.6)+ # geom_text(aes(label = gene))+ scale_color_manual(breaks = c('up','down','non'),values = c("#BC3C28","#0072B5","grey")) + geom_hline(aes(yintercept=-log10(0.05)),colour="grey",size=1 ,linetype=2) + #增加水...
The real-time PCR results were analyzed and expressed as relative miRNA expression of CT (threshold cycle) value, which was then converted to fold changes (19). The RT primer, PCR primers, and TaqMan probe for mir-21 (19) were purchased from ABI. U6 or 5S RNA was used for ...