Biomedical Engineering Reference
In-Depth Information
each of the lists were compiled and a single list of miRNAs produced. A dataset
consisting of
3500 microarray samples was also compiled to calculate correlation
values. The probesets on the chip targeting a miRNA host gene were identified. For
each host gene the Pearson correlation coefficient was calculated between the gene
and all other genes on the array for each dataset. The3%ofgenes with the largest
inverse correlation from each dataset were compiled into a list ranked on the number
of times a gene appeared. The HOCTAR method suffers from the fact that miRNAs
under investigation must result in mRNA transcript degradation and those targets un-
dergoing translation repression would not be detected. A database of HOCTAR target
predictions is available and can be searched by miRNA or gene name (Gennarino
et al.
2011
).
∼
3.4
Publicly Available miRNA Data Repositories
3.4.1
miRbase
miRbase is a web-based, searchable database designed to provide access to miRNA
sequences and annotation along with links to miRNA expression profiling data via
NCBI GEO (Kozomara and Griffiths-Jones
2011
). The database contains both hairpin
precursor miRNA and mature miRNA sequences. At the time of writing the latest
version, mirBase 18 contained 18,226 hairpin precursors and 21,643 mature miRNA
sequences from 168 species.
3.4.2
microRNA.org
microRNA.org (Betel et al.
2008
) provides a tool to study predicted miRNA targets
and miRNA expression in human, mouse and rat. Target predictions are acquired
from the miRanda algorithm and a more recent approach using a machine learn-
ing algorithm—miRSVR. Sequences for miRNA prediction from three mammalian
species (human, mouse and rat) are acquired from mirBase and the UCSC genome
browser. miRNA expression profiles are derived from next generation sequencing
studies of human, mouse rat and cell lines from
∼
250 small RNA libraries (Landgraf
et al.
2007
).
3.4.3
MicroCosm
Microcosm (http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/) is a
regularly updated database of predicted targets from miRanda provided by EMBL-
EBI. MicroCosm v5 contains target predictions for mirBase sequences against the
latest builds for EnsEMBL across 22 species' genomes. The user can search for
Search WWH ::
Custom Search