Computational protocol: Characterization of microRNA expression profiles in normal human tissues

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Protocol publication

[…] Genomic sequence of miRNA cluster and the predicted transcription factor binding sites were extracted from the "Cis-element clusters within BlastZ Aligments" option at the GenomeTraFac []. Tissue distribution of selected genes was derived from the GNF database [], in which the expression data from the same tissue types examined in our study were extracted for analyses. Target genes of miRNAs were predicted using the miRanda open-source software [] associated with the miRBase [] with a cutoff p value less than 0.05. The IGTC database [] was used to search the phenotype of mice carrying loss-of-function mutations. […]

Pipeline specifications

Software tools LASTZ, MiRanda
Databases miRBase GenomeTrafac IGTC
Application Nucleotide sequence alignment
Organisms Homo sapiens