Ongoing microRNA data analyses

Geuvadis meeting July 2012Marc Friedländer and Esther Lizano

Xavier Estivill labProgramme 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

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Some summary statisticsMinimum Median Maximum

Total reads ~1,000,000 ~12,000,000 ~50,000,000

quality filtered 0% 0.01% 2.3%

length filtered 0.5% 1.2% 81%

not mapped 1.9% 3.7% 75%

mapped 15.4% 95.1% 97%

annotated 88% 96% 98%

miRNAs 2% 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)

AcknowledgementsEstivill labXavier EstivillEulàlia MartíEsther Lizano

Roderic Guigo labPedro FerreraDavid Gonzales

Leiden University Medical CenterHenk Buermans

University of Geneva Medical SchoolTuuli Lappalainen

IMPPCLorena Pantano