Computational protocol: Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression

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Protocol publication

[…] miRNA expression data (small RNA sequencing) were used to extract miRNAs with negative correlation with their targets using the common samples (Supplementary Table ). Predicted targets of miRNAs were downloaded from miRWalk 2.0 database using the following parameter values: Input parameters Promoter 2 kb, 3′ UTR, minimum seed length 7 and/or p-value 0.05. We considered mRNA to be a target for miRNA if targeting was predicted by 2/3 of the databases miRanda, PICTAR2, and Targetscan–. Differentially expressed miRNAs were defined as having an absolute median ratio between two conditions >1.5, and the Benjamini-Hochberg adjusted p-value of a non-parametric Wilcoxon test <0.05. miRNAs were considered unexpressed if all samples had read count below 8 and they were excluded from differential expression analysis. Spearman’s rank correlations were calculated between the miRNA expression and the expression of its predicted targets with a threshold for negative correlation < = −0.50. For enrichment analysis, hypergeometric test was used to test statistical significance (p-value < 0.05) of the number of negatively correlating predicted targets of a miRNA. miRNA—target associations were visualized as circos plot using POMO. […]

Pipeline specifications

Software tools PicTar, TargetScan, POMO
Application sRNA-seq analysis
Chemicals Citric Acid