Computational protocol: The miR-200 family is increased in dysplastic lesions in ulcerative colitis patients

Similar protocols

Protocol publication

[…] Experimentally validated target genes for candidate miRNAs were obtained using miRTarBase,[] which contains targets that have been validated by reporter assays, western blot, qPCR, microarray and next-generation sequencing experiments. miRNA-target interactions were also investigated based on the collective information of functional studies of miRNAs in the database. To bioinformatically predict target genes based on the miRNA seed sequence, two predictive algorithms were used, TargetScan as well as miRDB.[,]To investigate the influence of candidate miRNA transcript levels in UC dysplasia, we interrogated the gene signatures obtained by cDNA microarrays in 4 UC patients without dysplasia and 11 UC patients harbouring remote neoplasia.[] To obtain a list of all differentially expressed genes across the two groups, the microarray datasets were obtained from the GEO repository (accession number GSE37283) and analysed with GEO2R, a web-based application that performs comparisons between groups on the original submitter-supplied microarray datasets. GEO2R uses the GEOquery and limma R packages from the Bioconductor project. For consistency, to identify differentially expressed genes, we applied the following thresholds: adjusted p-value < 0.05 (based on the Benjamini & Hochberg false discovery rate method) and |log2(fold-change)| > 1. […]

Pipeline specifications

Software tools TargetScan, GEO2R, GEOquery, limma
Databases miRDB miRTarBase
Application Transcription analysis
Organisms Homo sapiens