A:The idea behind miRror Suite is to examine the combinatorial affect of miRNAs working together in a wide variaty of situations. It is suggested that you read the detailed documentation and the tutorial
A: The current version supports 6 organisms ¿ Human, mouse, fly, rat, worm and zebrafish. Remember that the information in terms of tissue expression and supporting DBs is limited for some of the se organisms. It is suggested that you read the detailed documentation and the tutorial.
A: The basic functionality of miRror remains the same. However, 3 more organisms and 3 more DBs have been added. In addition, two more features have been added: miRorNet (dissconnection of regulatory pathways by miRNA triplets) and Psi-miRror (Probability Supported Iterative miRror). It is suggested that you read the detailed documentation and the tutorial
A: By selecting the genome of interest, miRror provides you with a set of Resources that are appropriate for the genome you have selected. These are major resources available with global predictions. Statistics with number of microRNAs and Targets for each resource is provided in the documentation and tutorial. All these DBs are show in the Links section
A: The best is to try and get familiarized with our tools. We recommend using our Recommended Set. You can select a Minimal Set of any combination of DBs. Recall that selecting more DBs only will only increase the number of predictions.
A: The resulting table will lead you to a more detailed table (use the question mark symbol). This "zoom" table will show you for each set of targets how many sites were identified by the selected Resources.
Recall that the number of sites was not included in the analysis.
A: The resulting table will lead you to a more detailed table (use the question mark symbol). This "zoom" will show you for each micorRNA how many Targets were identified from your input set by the selected DBs. Recall that the number of sites was not included in the analysis.
A: In this case, you may use miRror to lead you to ANY of the major sites that are reported and you can just go through the relevant links to these specialized Resources. In most cases, these DBs often contain richer information.
A: In this case, you may use miRror to lead you to ANY of the major sites that are reported and you can just go through the relevant links to these specialized Resources. However, we provide a linked connection to UniProt ID that is a rich source for the indicated protein.
A: The colors denotes levels of confidence marked by yellow (less likely) to red (more likely). The confidence levels indicate the likelihood that a specific miRNA (or the specific Gene-Target) are likely to be affected by the list of your input set (miRNAs or the Gene-Targets).
A: At this point, miRror does not support sequence or positional information. You should be using external source to convert these sequences to any formal identifier.
The currently available version of miRanda is a good starting point. miRanda will allow you to upload a list of miRNA sequences and a list of Gene-Target sequences in FASTA format.
A: Yes, we support download on miRror. You can download the results in tab delimited txt or Excel format. We also provide a direct link to PSI-miRror for a further refinement.
A: We provide the 'Reanalyze' option for changing the parameters (P-value cutoff, minimal number of databases or minimal number of hits per target). You might want to use a lower P-value and to restrict the search by forcing higher threshold for number of DBs and number of hits per target.
You may also use 'Filter option' to limit the resulting page by any of your favorite parameters.
A: Expand the databases used for the analysis. Also, you are encouraged to change the parameters (p-value cutoff, minimal number of databases or number of hits per target). You might want to use a relaxed threshold for p-value, a less restricted threshold for number of DBs or for the number of hits per target.
A: TarBase is the most exhaustive resource that was experimentally validated. It provides miRNAs that were shown in the lab to pair with their genes. In case TarBase validated miRNA-Targets are included in your set tested, it will be highlighted.
A: In the Simple mode, changing parameters will only filter the current results. You may only use parameters and thresholds that are more restricted. The results are always a subset of the initial list.
In the Advanced mode, you may change the parameters and will often get unseen results. Specifically, the results are according to the new set of parameters you have selected (P-value threshold, number of databases and number of hits). Of course you may change only some of the parameters in each run.
A: We provided you some shortcuts for gaining biological insights. Your results can be forward to major tools including DAVID, Reactome, STRING, PANDORA. However, you are encouraged to download the table results and use the information for any further analysis.
The core of the system is called miRtegrate. miRtegrate calculates the probability of matches between miRNAs in the user list as compared to all miRNAs that are reported for each of the database resources.
For simplicity we describe it with the miRNA input mode (but it is symmetrical for input of gene-targets). For each gene, we took into account the list of miRNAs that were associated with it per database. We calculated the probability of the genes interaction with the miRNAs in the user set as opposed to the rest of the miRNAs in that database. Calculating the P-value for miRNAs as input was performed for each predicting resource separately and according to the hypergeometric distribution. Formally, N is the total number of miRNAs in the database, n is the number of miRNA matches to the specific gene, k is the number of genes matches to miRNAs that appear in the user set, and m is the total number of miRNAs in the user set. Therefore, for each gene, the probability of X matches with miRNAs in the user set is:
We used a default value of 0.05 for the P-value filtration. To compile with P-value definition (i.e., achieving at least this value under the suggested distribution), we calculated the P-value by considering all probabilities that are more significant that the pre set threshold. The P-value is calculated for all cases that result with the pre-selected P-value of better. The same principle is applied with genes as input, resulting in a ranked list of miRNAs.
When different tissues and cell lines are used as a background, a new calculation for the P-value is activated by miRtegrate to account for the apparent different in coverage. miRror reports and ranks the gene-targets according to the most significant P-value obtained by any of the supporting databases. Detailed information is provided via the download options that show the actual number of binding sites found for each target according to the selected databases.
A: Indeed you can. You may activate the miR2Gene mode. The miRNAs that you found to be important are the input. You can use the top ranking scores of each of the DBs and any filter that is relevant to your experiment.
A: Indeed you can. You may activate the Gene2miR mode. The genes that you found to be important are the input. You are encouraged to restrict the analysis to genes expressing only in MIN6 cells. You can use the top ranking scores of each of the DBs.
Recall that when different tissues and cell lines are used as a background, a new calculation for the P-value is activated by miRtegrate to account for the apparent different in coverage. miRror reports and ranks the gene-targets according to the most significant P-value obtained by any of the supporting DBs. Detailed information is provided via the download options.
A: miRror has support for windows and firefox, but we recommend working on firefox if possible.
A: There is no formal limit but we suggest limiting the input to 200 molecules. Remember that the analysis can take much longer. In cases where the output becomes very large, only the first 200 targets will be displayed on the screen (the exact output number will be displayed as well)