Direction:
Please select tissue(s) for sample selection. Users can use Shift or Ctrl to select multiple options.

Mature miRNA Information:
The novel miRNA user provided is found in the YM500v2 database. The expression profile in tissues and the distribution of sample counts on expression (RPM) are shown in two figures. We applied three algorithms for predicting novel miRNAs: miRanalyzer, miRDeep2 and Mireap. The target prediction results are produced from two computational approaches: miRanda and TargetScan.

Precursor miRNA(s) Information:
The mature miRNA shown above most likely belongs to the pre-miRNA(s). The structures of the pre-miRNAs (stem-loop sequence) are plotted by RNAfold. The genomic regions of the pre-miRNAs are represented by three main customized genome browsers such as Ensembl, UCSC and NCBI.

Direction:
Please select a pre-miRNA and press the IsomiR Performance button to represent the miRNA isoforms.

References:

1. miRDeep2: Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N, (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40(1):37-52.
2. Mireap: Chen X et al., (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol. 10(7):R78.
3. miRanda: http://www.microrna.org/microrna/home.do
4. TargetScan: http://www.targetscan.org/vert_50/seedmatch.html
5. RNAfold: Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P, (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188.
6. Ensembl: Flicek P et al., (2012) Ensembl 2012. Nucleic Acids Res. 40(Database issue):D84-90.
7. UCSC: Kent WJ et al., (2002) The Human Genome Browser at UCSC. Genome Res. 12(6):996-1006.
8. NCBI: Wheeler et al., (2003) NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/mapview).

Direction:
The miRNAs found in the YM500v2 or user provided are shown here. Please select miRNAs (default: all selected) after tissues are already selected, or the checkboxes cannot be selected (disabled).

Direction:

1. Nucleotide substitution  : How many mismatched bases are miRNA isoforms allowed to align the mature miRNA by? Default: 1.
2. Read count  : How many reads do miRNA isoforms have to be supported by? Default: 100.
3. Sample count  : How many samples do miRNA isoforms have to be supported by? Default: 5.
4. Nucleotide trimming/addition variation: Whether the sequences of the 3 prime and 5 prime miRNA isoforms should be added/trimmed or not? (Default: allow the sequences of both the 3 prime and 5 prime miRNA isoforms to be added and trimmed)
5. Editing rate: How many percentage of reads can support putative miRNA editing for each base? (Default: 10)
6. Including flanking region site: Whether the putative miRNA editing bases include flanking region site? (Default: the putative miRNA editing bases do not include flanking region site)

 Note that, the web system would spend more time performing miRNA isoforms while the first (1) option is set to higher, the second (2) or the third (3) option is set to lower.

Direction:
Please select a pre-miRNA and press the IsomiR Performance button to represent the miRNA isoforms after all options are already set below.

Direction:
Please select a pre-miRNA and press the Arm-switching Expression button to perform the results.