To download the user manual, click here
I. Main page
II. Search results
III. Detailed results
I. Main page
Main Menu (clickable image)
Main menu bar
Button Description
Home To return to vHoT DB home
FAQ To move to the 'Frequently Asked Questions' page
Help To view detailed descriptions of vHoT DB menus and terms (this page)
Demo To view a simple demo about how to use vHoT DB
About To view a brief introduction to vHoT DB
mRNA species selection
This menu is to select target mRNA species. Only the species selected here will be included in the search result. Currently, vHoT supports the following species:
  • Human
  • Mouse
  • Viruses
  • Cow
  • Rat
  • Rhesus Monkey
  • Viral miRNA selection
    This is to select the viral miRNA of interest. You can select a viral miRNA from over 270 mature miRNAs of over 17 species listed in miRBase. There are two ways of selecting a viral miRNA. One way is to use the two-step dropbox (this is the default). The other is to enter the name or accession ID of the viral miRNA directly. More details of the miRNAs used by vHoT can be found in miRBase.
    To select a viral miRNA using the two-step dropbox
    1. Check 'Select an item from dropbox' (default)
    2. Select a virus type from 'Select an organism' dropbox
    3. From 'Select a miRNA' dropbox, select a viral miRNA among the list of miRNAs which are derived from the viral species chosen from step 2
    To select a viral miRNA by entering its name or accession ID
    1. Check 'Type a name'
    2. Enter the name or accession ID of a viral miRNA
    Advanced Options
    This menu is to set up parameters for more advanced search. You can select the types of algorithms you will use, how result will be summarized, and specific parameters of each algorithm. You can also specify the target genes by entering their accession IDs.
    Algorithm Selection | This is to select the algorithm(s) to predict candidate mRNA targets of miRNA. vHoT DB supports TargetScan, miRanda, and RNAhybrid, and you can select multiple algorithms for analysis. A brief description of each algorithm is as follows:
  • TargetScan (Lewis et al., 2003) predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA by calculating thermodynamic free energy using the RNAFold package (Hofacker, 2003). Predictions are ranked using the site number, site type, and site context, which includes factors that influence target-site accessibility. More details can be found at http://genes.mit.edu/targetscan.
  • miRanda (Enright et al., 2003, John et al. 2004) uses sequence complementarity (using a position-weighted local alignment algorithm), free energies, and conservation of target sites to predict miRNA-mRNA interactions. Further details can be found at http://www.microrna.org.
  • RNAhybrid (Rehmsmeier et al., 2004) is an extension of classical RNA secondary structure prediction software tools such as RNAfold (Hofacker, 2003) and Mfold (Mathews et al., 1999). RNAhybrid finds the minimum free energy hybridization of a long and a short RNAs to predict target mRNA-miRNA interactions. For further information, please refer to the RNAhybrid web site.
  • DIANA microT (Maragkakis et al., 2009) uses miTGs (miRNA target gene score) by combining conserved and non-conserved MRE (miRNA Recognition Element) score to predict miRNA-mRNA interactions. Detailed information can be found at http://diana.cslab.ece.ntua.gr.
  • PITA (Kertesz et al., 2007) uses difference between the binding free energy of the miRNA-target duplex structure and the energetic cost of unpairing the target-site nucleotides to predict miRNA-mRNA interactions. For further information, please refer to http://genie.weizmann.ac.il
  • Select a post processing | This is to specify how results will be summarized. Select 'Intersection' (this is the default option) if you want to view the search results commonly predicted by all three algorithms. Select 'Union' if you want to see the list of target mRNAs predicted by at least one algorithm (i.e., any of TargetScan, miRanda, RNAhybrid, DIANA microT and PITA).
    Minimum Free Energy (MFE) threshold option | If you use miRanda or RNAhybrid, you can set the MFE threshold. These algorithms select only those miRNA-mRNA pairs whose MFE is below the specified threshold.
    The default values are -10kcal/mol for miRanda and -20kcal/mol for RNAhybrid. These default values were chosen by referring to the MFEs of the experimentally validated miRNA-mRNA duplexes. More details can be found in the answers to Q18 and Q19 in the FAQ page.
    Total context score threshold option | If you use TargetScan, you can set a parameter called the total context score threshold. TargetScan specifically chooses the targets whose context scores are above the specified threshold.
    The default value is -1, which was chosen by referring to the total context score of the experimentally validated targets. More details can be found in the answers to Q18 and Q19 in the FAQ page.
    Score threshold option | The search result by DIANA microT can be restricted by setting a score threshold. If you set a score threshold, DIANA microT selects out miRNA-mRNA pairs whose scores are above the specified threshold. The minimum (and default) value is 7.3.
    ddG threshold option | The search results by PITA can be limited by setting a ddG threshold. If you set a ddG threshold score, vHoT selects the miRNA-mRNA pairs whose scores are below the specified threshold and only shows the screened test results. The default value is chosen by regarding the number of results taken into account.
    Target gene(s) | This is to limit vHoT search to the target sites of user-specified genes instead of the entire genome. Enter a comma-separated list of mRNA accession IDs of interest into the 'Target gene(s)' box. mRNA accession IDs can be obtained from the NCBI web site.
    Search and Reset button
    Search | To begin search
    Reset | To go back to initial mode
    II. Search results
    Search results (clickable image)
    Table for miRNA in query
    This table displays basic information on the miRNA in query such as its accession ID, mature sequence and seed sequence.
    Property Description
    Accession ID The official accession ID of the miRNA in query. This accession ID is from miRBase. For more information on this miRNA, click on miRNA accession IDs, which will direct you to the corresponding miRNA page in miRBase.
    Name The name of the viral miRNA in query
    Sequence The nucleotide sequence of the viral miRNA in query
    Seed The seed sequence of the viral miRNA in query
    Total number of predicted targets
    This represents the number of target mRNAs shown in the current page and the total number of target mRNAs
    Page index
    The number shown in bold represents the current page number.
  • Click on any number to directly move to the corresponding page.
  • Click on NEXT to move to the next page.
  • Click on PREV to go to the previous page.
  • Output display options
    Test results can be sorted with respect to Gene ID, Species, TargetScan, miRanda, RNAhybrid, DIANA microT, or PITA and re-displayed. The number of mRNA outputs per page can also be controlled.



    Sort by
    Gene ID To sort the result with respect to Gene ID in ascending order
    Species To sort the result with respect to the species in the order of self, human and mouse
    TargetScan Count To sort TargetScan instances with respect to the number of targets sites in descending order
    miRanda Count To sort miRanda instances with respect to the number of targets sites in descending order
    RNAhybrid Count To sort RNAhybrid instances with respect to the number of targets sites in descending order
    DIANA microT Count To sort DIANA microT instances with respect to the number of targets sites in descending order
    PITA Count To sort PITA instances with respect to the number of targets sites in descending order
    TargetScan Score To sort TargetScan instances with respect to the score of targets sites in descending order
    miRanda Score To sort miRanda instances with respect to the score of targets sites in descending order
    RNAhybrid P-value To sort RNAhybrid instances with respect to the p-value of targets sites in ascending order
    DIANA microR Score To sort DIANA microT instances with respect to the score of targets sites in descending order
    PITA ddG To sort PITA instances with respect to the ddG value of targets sites in ascending order
    Per Page
    To control the number of items shown per page.
    Choose one of 10, 40, 100, 500, 1000.
    Remote Control Panel
    You can use the remote control panel (appearing in the right side of each page) in order to easily navigate over pages.
    Button Description
    To move to the first page
    To go to the previous page
    To go to the next page
    To move to the last page
    Page To enter the page number you want to go to
    Go To go to the page specified in the 'Page' box
    top To move to the top of the current page
    bottom To move to the bottom of the current page
    Target mRNA result table
    This table shows the search results obtained from running TargetScan, miRanda, and RNAhybrid. The table has five columns, one for each of Gene ID, Species, TargetScan, miRanda, RNAhybrid, DIANA microT and PITA.
    Gene ID The gene accession ID assigned by NCBI. Further information on each gene can be found by clicking on the ID, which will lead you to the corresponding page in the NCBI web site.
    Species The origin of target mRNA (i.e., human, mouse or self)
    TargetScan The 'Detected' term indicates that some mRNA-miRNA pairing site(s) have been detected by the TargetScan algorithm. The number shown after 'Detected' represents the number of detected sites within the gene in a row. To see more detailed information, you can click 'Detected'. You can also download the result in the CSV (comma separated value) format by clicking the disk icon () appearing next to the TargetScan column heading. A spreadsheet program such as Microsoft Excel can be used to open a CSV file.
    miRanda You can examine the search result from miRanda in a similar way.
    RNAhybrid You can examine the search result from RNAhybrid in a similar way.
    DIANA microT You can examine the search result from DIANA microT in a similar way.
    PITA You can examine the search result from PITA in a similar way.
    Top results and DB statistics
    This page shows three pieces of information: (1) some important statistics calculated over the entire database, (2) top 10 results for each prediction algorithm, and (3) total ranking of predicted results in terms of a composite score calculated from 5 individual scores. More details are as follows:
    DB statistics | For rapid responses, vHoT precomputes the score of each mRNA-miRNA pairing and stores the result. This table shows the statistics related to this precomputation such as the number of mRNA-miRNA duplex records, the mean and standard deviation of the score each prediction algorithm reports.
    Top 10 results | For each prediction algorithm, top 10 prediction results are presented. The accession ID and taxonomy ID (species ID) of each target gene and miRNA-mRNA duplex score are shown. (More details of taxonomy ID can be found at http://www.ncbi.nlm.nih.gov/taxonomy.) For instance, the table below shows the top 10 results for hiv1-miR-H1 reported by TargetScan.
    Total ranks | By combining the scores produced by each prediction algorithm, vHoT computes a composite score for each result and ranks the predicted targets with respect to this composite score (up to 10 results are shown). Since different algorithms report their scores in different signal ranges, normalization is needed for computing a composite score. We thus normalize the scores reported by each algorithm in terms of the standard z-score and then calculate a linear sum of the resulting z-scores as the composite score. Up to 10 genes that have the highest composite scores are shown in the table. Since RNAhybrid and PITA use the negative energy values as the scores, we multiply their scores by -1 first and then cumulate them to get the final composite score.
    III. Detailed results
    This is to show more detailed search results obtained from running TargetScan, miRanda, and RNAhybrid. The definition of each attribute term appearing in this page can be found by hovering your mouse cursor over the term. A pop-up help window will appear, showing the description of each term.
    TargetScan
    Gene ID The gene accession ID assigned by NCBI. Further information on each gene can be found by clicking on the ID, which will lead you to the corresponding page in the NCBI web site.
    Species The origin of target mRNA (i.e., human, mouse or self)
    miRNA ID The official accession ID of the miRNA in query. This accession ID is from miRBase. For more information on this miRNA, click on miRNA accession IDs, which will direct you to the corresponding miRNA page in miRBase.
    Site type The site of miRNA which forms base-pairing with target mRNA is classified as 7mer-1a, 7mer-m8, or 8mer.
  • 7mer-m8: An exact match to positions 2-8 of the mature miRNA (the seed + position 8)
  • 7mer-1A: An exact match to positions 2-7 of the mature miRNA (the seed) followed by an 'A'
  • 8mer: An exact match to positions 2-8 of the mature miRNA (the seed + position 8) followed by an 'A'
  • UTR Start position The nucleotide position of the UTR that starts to form base-pairing with position 8 or position 7 of the mature miRNA.
    UTR end The nucleotide position of the UTR that forms base-pairing with position 2 of the mature miRNA.
    3' Pairing Contribution The consequential miRNA-target complementarity outside the seed region. A more negative score is associated with a more favorable site (Grimson et al., 2007).
    Local AU Contribution The transcript AU content 30 nt upstream and downstream of predicted site. A more negative score is associated with a more favorable site (Grimson et al., 2007).
    Position Contribution The distance to the nearest end of the annotated UTR of the target gene. A more negative score is associated with a more favorable site (Grimson et al., 2007).
    Total Context Score The sum of the contribution of site-type contribution, 3' pairing contribution, local AU contribution, and position contribution.
    Context Score Percentile The percentage of sites for this miRNA with a less favorable context score.
    UTR pairing The base pairing pattern between miRNA and 3' UTR of target mRNA.
    miRanda
    Gene ID The gene accession ID assigned by NCBI. Further information on each gene can be found by clicking on the ID, which will lead you to the corresponding page in the NCBI web site.
    Species The origin of target mRNA (i.e., human, mouse or self)
    miRNA ID The official accession ID of the miRNA in query. This accession ID is from miRBase. For more information on this miRNA, click on miRNA accession IDs, which will direct you to the corresponding miRNA page in miRBase.
    Score The optimized complementarity score between a miRNA sequence and an mRNA sequence (typically a 3' UTR) calculated by miRanda algorithm. For detailed information on scoring rule, please refer to Enright et al., 2003.
    Free Energy The thermodynamic free energy of a miRNA - mRNA duplex
    Align Length The length of an alignment including gaps
    UTR Start position The first nucleotide position of UTR which begins to form base-pairing with miRNA
    UTR end The last nucleotide position of UTR which forms base-pairing with miRNA
    miRNA start The first nucleotide position of a miRNA that forms base-pairing with target mRNA
    miRNA end The last nucleotide position of a miRNA that forms base-pairing with target mRNA
    ID Value The percentage of the number of total base pairs excluding wobble pairs divided by align length
    Similar Value The percentage of the number of total base pairs including wobble pairs divided by align length
    UTR pairing The base pairing pattern between miRNA and 3' UTR of target mRNA.
    RNAhybrid
    Gene ID The gene accession ID assigned by NCBI. Further information on each gene can be found by clicking on the ID, which will lead you to the corresponding page in the NCBI web site.
    Species The origin of target mRNA (i.e., human, mouse or self)
    miRNA ID The official accession ID of the miRNA in query. This accession ID is from miRBase. For more information on this miRNA, click on miRNA accession IDs, which will direct you to the corresponding miRNA page in miRBase.
    Target Length The length of the target mRNA in nt
    miRNA Length The length of the miRNA in nt
    MFE Minimum Free Energy which represents the free energy of a predicted miRNA - target mRNA duplex in kcal/mol.
    P-value The p-value is based on extreme value distributions of length normalized energies.
    Position The starting position of the alignment in the target mRNA
    UTR pairing The base pairing pattern between miRNA and 3' UTR of target mRNA.
    DIANA microT
    Gene ID The gene accession ID assigned by NCBI. Further information on each gene can be found by clicking on the ID, which will lead you to the corresponding page in the NCBI web site.
    Species The origin of target mRNA (i.e., human, mouse or self)
    miRNA ID The official accession ID of the miRNA in query. This accession ID is from miRBase. For more information on this miRNA, click on miRNA accession IDs, which will direct you to the corresponding miRNA page in miRBase.
    Gene Description This contains official full name, encoding protein, and source.
    Score The final prediction score. A higher score corresponds to higher possibility of being a real target. A non-strict (default) threshold is set at score 7.3 and a strict threshold at score 19.
    Binding Score Defines how much each binding site on the UTR contributes to the overall score.
    Binding Category Shows the number of nucleotides that bind in the first 9 nt of the alignment and whether there are any G:U wobble pairs.
    UTR Position The position of the target site on the 3’UTR. It may be used to easily see distances between target sites on the same 3’UTR and distances from the end of the coding region.
    Position on Chromosome The target site position on the chromosome.
    UTR pairing The graphic representation of the binding between the miRNA and the target site.
    PITA
    Gene ID The gene accession ID assigned by NCBI. Further information on each gene can be found by clicking on the ID, which will lead you to the corresponding page in the NCBI web site.
    Species The origin of target mRNA (i.e., human, mouse or self)
    miRNA ID The official accession ID of the miRNA in query. This accession ID is from miRBase. For more information on this miRNA, click on miRNA accession IDs, which will direct you to the corresponding miRNA page in miRBase.
    Position The position of the target site on the 3' UTR.
    Seed PITA's "X:Y:Z" notation for describing the seed represents the size of the seed (X), the number of mismatches (Y) and the number of G:U wobble pairs (Z). For example, 8:0:1 means that the seed is an 8-mer, has no mismatches but contains a single G:U wobble.
    dG duplex dG-duplex is the binding free energy of the miRNA-target duplex structure in which the miRNA and target are paired according to pairing constraints imposed by the seed (Kertesz et al., 2007).
    dG open dG-open is the free energy lost by unpairing the target-site nucleotides (Kertesz et al., 2007).
    ddG ddG is the total miRNA-target interaction score that is equal to the difference between dGduplex and dGopen (Kertesz et al., 2007).

    top