Ongoing microRNA data analyses Geuvadis meeting July 2012 Marc Friedländer and Esther Lizano Xavier Estivill lab Programme for Genes and Disease Center for Genomic Regulation (CRG)

Basic analyses pre-processing mapping (bowtie format) annotation break-down improved miRNA strand annotation miRNA variant sequence annotation quantification of miRNAs and variants QC (phred scores) control for contamination length profiling visualization (bedGraph) summary statistics )(

Advanced analyses identification of novel miRNAs with miRDeep2 QC (based on PCA) allele-specific expression eQTL / correlation with DNA variants correlation with mRNA expression …… ) ( ) (

Some summary statistics MinimumMedianMaximum Total reads~1,000,000~12,000,000~50,000,000 quality filtered0%0.01%2.3% length filtered0.5%1.2%81% not mapped1.9%3.7%75% mapped15.4%95.1%97% annotated88%96%98% miRNAs2%6%62% - we detect 1615 out of 1921 known human miRNAs (>84%) - we profile ~400 miRNAs robustly (detect them in >90% of the samples)

Novel human miRNA candidates identified by miRDeep2 - we identify 257 novel human miRNA candidates - of these 64% are computationally estimated to be genuine - we recover 74% of the known human miRNAs in the data - (incidentally we also recover 23/25 (92%) Epstein Barr virus miRNAs) - visual inspection reveals some false positives, more filtering required…

Correlations between miRNA and mRNA target expression (CLL consortium data)

miRNA switches and tuners - switches turn off the expression of their targets - tuners fine-regulate the expression of their targets - switch target expression should be very low - tuner target expression should be in the physiologically relevant range Figure from Lai, Current Biology 2005

Expression of mRNA targets and non-targets (CLL consortium data)

Acknowledgements Estivill lab Xavier Estivill Eulàlia Martí Esther Lizano Roderic Guigo lab Pedro Ferrera David Gonzales Leiden University Medical Center Henk Buermans University of Geneva Medical School Tuuli Lappalainen IMPPC Lorena Pantano