Software

miRNAVISA

The term miRNAVISA derives from a concatenation of miRNA and VISA. The term VISA connotes both the “visualizations” of data to allow easy correlation of analyzed variables (species, chromosomes, miRNA families) and “entry” into the exciting miRNA world.

• Getting Started

• Inter-species Comparisons

  Under this menu, the user can select a combination of two or more species together with at-least two families. The user can also opt to use the automated selection buttons for the popular (in terms of miRNA gene numbers) species vis-a-vis the largest miRNA families in the latest release of the miRBase database i.e., the central repository for miRNA research. In the example below, chicken (Gallus gallus) and mouse (Mus musculus) are selected with the combination of the miRNA families mir-515, mir- 548, mir-466 and mir-663. The user can select a species or miRNA family by clicking on the respective buttons with their names.

  After submitting the query, the program generates graphical output in the Scalable Vector Graphic (SVG) format. Two buttons are provided for either download or display of the graph. By clicking on the “Download graph” button user can download a compressed SVG picture and by clicking on the “Display graph” the program opens a new window with the graph (see below) for perusal. The graph shows comparisons of miRNA gene distribution based on user input of miRNA families and species, relative to all other species in the miRBase database.

Inter-species comparison

The results above imply that:

1. This figure summarizes the data at miRBase [Release 19 (R19), dated August 2012]. The miRBase R19 database contains 21,264 miRNA genes from 193 species as indicated on the y-axis.
2. There are 15,554 (298+15256) family-annotated miRNA genes in the miRBase R19 that belong to 1,543 miRNA families. Only 298 miRNA genes belonging to the four selected families are analyzed and summarized in this figure.
3. This figure shows the distribution of miRNA genes in the miRNA families indicated on the x-axis across the 193 species.
4. The output from miRNAVISA indicates that none of 150, 116 and 16 miRNA genes annotated to the miRNA families mir-515, mir-548 and mir-663, respectively, belong to the two species. In fact, these families may only be specific to primate species as illustrated in Figure 3b (below) and elaborated in the manuscript.
5. All the 16 miRNA genes belonging to the miRNA family mir-466 are is specific to mouse and chicken but a majority (94%) of these have been observed in mice (Mus musculus). Only one family gene has been annotated in the chicken genome (Gallus gallus).

Sample results given a miRNAVISA inter-species comparison query (four families).

• Intra-Species Comparison

  The Intra-species comparisons menu offers the same user interface as the inter-species comparison menu. However, the intra-species comparisons menu only allows the selection of one species and at-least two but no more than 50 miRNA families. The user can also opt to use the automated selection buttons for the human genome (default genome) to assess the distribution of miRNA genes belonging to the largest (top) miRNA families which are specific only to the selected genome. The graphical output, a genome miRNA genes/family map, shows the chromosomal distribution (rows) and per-family distribution (columns). The miRNA genes that are not mapped to any chromosome are reported under a predefined label ‘Chunks/NoMap’. The figure below illustrates the genomic distribution of family-annotated miRNA genes in the human genome

Sample results given a miRNAVISA intra-species comparison query. Genomic distribution of family-annotated human miRNA genes in the 50 largest miRNA families.

There are 1600 registered human miRNA genes in miRBase R19. About 61.2% (367 plus 612 genes) are classified into different miRNA families. The figure shows genome-wide distribution of miRNA genes in the 50 largest miRNA families. Moreover, it is apparent from the figure that:

• The most populous miRNA family in human genome is mir-548 and its genes are spatially located in different chromosomes.
• Most human miRNA genes are located in chromosomes 1 (135 genes) and X (113 genes).
• Genes in miRNA families mir-515 (chromosome 19), mir-154 (chromosome 14), mir-379, mir-743, mir-329, mir-368, mir-500, and say mir-188 are each co-located on a specific chromosome.
• Some co-located miRNA genes, on chromosome 14, in different miRNA families exist as a large cluster as explained in the manuscript.

Family Query:

The Family Query menu allows a keyword search based on standard miRBase nomenclature for the names of miRNA, miRNA genes, and their families. The names/keywords are case insensitive and can include:

• miRNA gene family name e.g. mir-515, or
• miRNA gene family name e.g. mir-515, or
• miRNA gene (hairpin) name e.g. hsa-mir-524 and hsa-mir-519a-2, and/or
• hairpin accession e.g. MI0003160 and MI0003182.

Sample results a given miRNAVISA keyword or family query.

An error message is returned for unsuccessful keyword queries. The output of a successful miRNA family query includes:

• A table showing the summary statistics for a searched keyword and detail of miRNA genes associated with the keyword such as expression trends and annotated functions, if any, of the functional ~22nt mature miRNA hosted on these genes(See the above image)
• A graph showing the distribution of family-specific miRNA genes across species associated to the searched keyword(See the figure below.)
• DNA strand preferences of miRNA genes in a given family associated to the searched keyword(See the last image)

Distribution of miRNA genes constituting the miRNA family “mir-515” in different species.

The figure above shows the distribution of miRNA genes with both known (mapped) and unknown (unmapped) chromosomal co-ordinates in each species. Figure 7 shows a comparison of the DNA strand preferences of mapped miRNA genes on the right panel. The number of miRNA genes that have been mapped on the positive (+1; FWD) strand and negative (-1; REV) strand are shown in red and blue bars, respectively. The number of unmapped miRNA genes in each species is reported on the left panel (green bars) in the figure below.

Strand preferences miRNA genes constituting the “mir-515” miRNA gene family. The right panel shows the DNA strand preferences and number of mapped miRNA genes in different species. The left panel shows the number of miRNA family “mir-515” genes with unknown chromosomal co-ordinates in each species.

The blue bars in the above figure are explained in the manuscript along with the inference that the miRNA family mir-515 are preferentially transcribed from the +1 DNA strand. All the miRNA families mir-515 genes have only been reported in primate species (Figure 6). The user can download all the results of a query for their own use. These results are packaged in one archive file. All the graphs are in the Scalable Vector Graphs (SVG) file format and the tables are “tab separated” files that can easily be imported into any spreadsheet programs.