MirZ web server

Category Cross-Omics>Knowledge Bases/Databases/Tools and Genomics>Gene Expression Analysis/Profiling/Tools

Abstract The MirZ web server provides the life science community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment.

The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens.

The smiRNAdb miRNA expression atlas --

smiRNAdb is a unique, web-accessible and widely used resource (database) of miRNA profiles determined by sequencing from hundreds of Homo sapiens, Mus musculus, Rattus norvegicus, etc. samples.

The web interface of smiRNAdb features an extended repertoire of on-line analysis (tools) such as visualization and hierarchical clustering of miRNA expression profiles, principal component analysis (PCA), comparison of miRNA expression between two (sets of) samples with the aim of identifying the miRNAs whose expression differs most between the samples.

The manufacturer used the Brenda tissue ontology as a guide in organizing the samples such that the user can readily identify related cell lineages or normal and pathological samples derived from a given tissue type.

The manufacturer’s tissue hierarchy has four (4) levels: the organ/system (e.g. hematopoietic system), subsystem (e.g. lymphoid lineage), cell type (e.g. B cell) and further cell type classification (e.g. B lymphocyte).

MiRNAs themselves can be analyzed independently, grouped by their 2-7 sub-sequence, or grouped in precursor clusters.

Two (2) miRNAs are placed in the same precursor cluster if their loci are within 50 kb of each other in the genome, or if they share a mature form.

MirZ web server Database & Tools --

1) smiRNAdb is a database containing expression information for human, mouse, rat, zebra-fish, worm and fruit-fly small RNAs (mostly miRNAs).

2) Visualization of MiRNA Profiles - Relative frequency of selected miRNAs across a selected set of samples.

3) Sample Comparison - Compare two (sets of) samples based on mature miRNAs, mature miRNA sequence groups or precursor clusters.

4) Custom Sample Comparison - Compare two (sets of) samples based on mature miRNA by uploading your own miRNA data.

5) Sample Clustering - Hierarchical clustering of samples based on counts of sequenced miRNAs.

6) Sample PCA - Visualize the relationships between samples using principal component analysis (PCA) and miRNA counts.

7) Downloads - Summary of annotation and copy number of sequences in samples from each species.

8) Sample Composition - Counts and frequencies of various functional categories of small RNAs present in the samples.

9) Sequence Search - Find sequences in the database that are homologous to a query sequence.

The ElMMo ‘miRNA target prediction’ algorithm based on comparative genomic analysis --

To be able to address the question of what mRNA is most likely affected by the change in expression of a miRNA, the manufacturer’s coupled smiRNAdb to a PHP-based web interface to the ElMMo miRNA target predictions.

The current release (3/09) of ElMMo features miRNA target predictions for H. sapiens, M. musculus, R. norvegicus, D. rerio, C. elegans and D. melanogaster.

Of these, the M. musculus and R. norvegicus predictions were Not present in the manufacturer’s initial publication.

Furthermore, for the remaining organisms, the current predictions are based on the genome sequences of a larger set of species, because more fully sequenced genomes became available since 2007.

The manufacturers further based their predictions on the most recent mRNA sequences and 3'-UTR annotations provided by the RefSeq database.

NCBI Reference Sequences - The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

RefSeq is a foundation for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.

Concerning the microarray profiles that the user can use to guide miRNA target discovery in specific tissues and aside from the H. sapiens profiles that were used in the original ElMMo release, the manufacturers incorporated similar mRNA expression profiles for M. musculus and R. norvegicus.

Finally, the ElMMo web interface now informs the user about the smiRNAdb samples in which the selected miRNAs are most strongly expressed.

The following additional major functions can also be accomplished through the Zavolan Lab / MirZ web server --

1) Computational prediction of microRNA genes using miR-abela to predict microRNA genes.

2) MBII-52 snoRNA target Predictions -

System Requirements

Contact manufacturer.


Manufacturer Web Site MirZ web server

Price Contact manufacturer.

G6G Abstract Number 20752

G6G Manufacturer Number 104334