Tutorial on how to use vHoT: using hiv1-miR-H1 as a query miRNA
2. Text version (the contents are the same as the video version)
Select species. In this tutorial, we use 'Human' as the target genomes.
For convenience, vHoT supports pop-up help. Just hover your mouse over the term of interest. A pop-up window will appear, showing the definition of or more information on the term.
Select Viral miRNA
hiv1-miR-H1 is derived from Human immunodeficiency virus 1. Select 'Human immunodeficiency virus 1' from the 'Select an organism' menu.
Then select 'hiv1-miR-H1' from the 'Select a miRNA' menu.
For further information on viral microRNAs and their host viruses, visit the miRBase web site
Set More Advanced Options
To further customize your search, you can use the advanced options menu. You can choose the type of algorithm to use for analysis (and change the algorithm parameters as well, as shown below). In this tutorial, we use the miRanda and RNAhybrid algorithms. Check 'miRanda' and 'RNAhybrid' in the 'Algorithm Selection' menu.
In order to view those mRNAs that are predicted by both miRanda and RNAhybrid, check 'Intersection.' Obviously, selecting 'Intersection' will return fewer results than selecting 'Union', which will return mRNAs that are predicted by any of the algorithm(s) used.
You can also adjust the parameters of the algorithm(s) used. The miRanda and RNAhybrid algorithms accept a parameter called MFE (minimum free energy) threshold. In this tutorial, let's use -20 for miRanda, and -20 for RNAhybrid. The unit is kcal/mol. Note that the number of mRNA targets in the result will be decreased as the value of MFE decreases.
We will make no changes in other parameters of an 'Advanced option' menu.
Click the 'Search' button to begin.
Check Results: Information on miRNA of Interest (hiv-miR-H1)
vHoT displays the data about the miRNA itself in query as well as target mRNAs in the result page. The top table shows the basic information on the query miRNA such as its accession ID and sequence. In this example, MIMAT0004480 represents the accession ID of hiv-miR-H1. If you click on this miRNA accession ID, you will be directed to the hiv-miR-H1 data page in miRBase and be able to easily retrieve detailed information on hiv-miR-H1.
Check Results: Information on Target Genes
The bottom table in the result page displays search results about target genes. Since we chose in this tutorial 'Human' as target species and 'miRanda' and 'RNAhybrid' as search algorithms, the resulting target genes are derived from human, and the search results by TargetScan, DIANA microT and PITA are left blank.
Let's take a look at the first candidate target gene. It is derived from human, and its gene ID is NM_000017. Within this gene, miRanda and RNAhybrid predict 1 target site.
Let's click on 'Detected (1)' in the miRanda column for more detailed search results by miRanda.
By hovering your mouse cursor over the attributes shown in this page, you can quickly check their definitions. For more information on miRanda, you can also refer to the original miRanda web site
Similarly, you can click on 'Detected (1)' in the RNAhybrid column in order to retrieve more detailed results by RNAhybrid.
Likewise, the definition of each term can be found in the pop-up help windows. You can also refer to the RNAhybrid web site
for more information on RNAhybrid.