A step-by-step guide to searching and retrieving data from TarMiR 1.0

How to retrieve lists of targets for microRNA/s using has-miR-1 as an example:

  
  1. To initiate the search, first click the ‘TarMiR tool’ link at the upper-right corner to bring up an intermediary page,  
  2. This page gives you two options, one for entering or pasting a list of miRNAs and/or mRNAs (recommended for small lists with less than 10 objects)      and the other one for uploading longer lists of miRNAs and/or mRNAs. Make your selection by clicking the appropriate link, .  
  3. In this example, we use the option to paste or enter the miRNA name (hsa-miR-1),  
  4. Select ‘MiRNA target prediction’ from the select prediction type drop-down menu,  
  5. Select species as Homo sapiens (in this case),.  
  6. Enter ‘Percentage cut-off’, i.e. the top “x” % ranked predictions from each server that you want to retrieve. Leaving the field blank will cause     TarMiR 1.0 to use the default value of 100%,  
  7. Enter or paste the miRNA name/s or miRBase accession number/s in the “Input one or more miRNAs” text box. In this case, enter miR- 1 in the     text box. Since the species has already been selected, entering the species identifier (hsa) is optional. When entering multiple miRNAs, make sure     that each line contains only one entry,  
  8. Alternatively if your list of miRNAs is large, you can use ‘ upload text file ’ option which can be accessed from the intermediary page described in     step 2. The text file can contain the miRNA names.  In the text file, each miRNA should be in new line (format e.g.: hsa-mir-1),  
  9. Select servers from which you want the pre-computed lists of targets, by clicking each or by using the selection tool (Select at least one server for     individual server prediction and select a minimum of two servers for ‘Comprehensive’ and ‘Shared targets’ Prediction),  
  10.  After you submit the selection, you will be directed to a page showing the links to detailed results. You can either view (in an html page) or             download the predictions from each individual server by clicking on the right option,  
  11. The comprehensive list gives you the non-redundant list of mRNA targets for your miRNA/s collected from the servers selected by the user,  
  12. The shared targets list, gives you only those targets for the miRNA that are common across the servers selected. This can be viewed as a high        confidence list because of the consensus predictions from multiple server,  
     

How to retrieve lists of miRNAs that are predicted to target a transcript/s or mRNA/s:

  
  1. To initiate the search, first click the ‘TarMiR tool’ link at the upper-right corner to bring up an intermediary page,  
  2. This page gives you two options, one for entering or pasting a list of miRNAs and/or mRNAs (recommended for small lists with less than 10 objects)      and the other one for uploading longer lists of miRNAs and/or mRNAs. Make your selection by clicking the appropriate link,  
  3. In this example, we use the option to paste or enter the mRNA/gene symbol,  
  4. Select ‘mRNA prediction’ from the select prediction type drop-down menu,  
  5. Select species as Homo sapiens (for instance!),  
  6. Enter ‘Percentage cut-off’, i.e. the top “x” % ranked predictions from each server that you want to retrieve. Leaving the field blank will cause     TarMiR 1.0 to use the default value of 100%,  
  7. Enter or paste the mRNA symbol (gene symbol) in the “Input one or more mRNAs” text box. When entering multiple mRNAs, make sure that each     line contains only one entry,  
  8. Alternatively if your list of mRNAs is large, you can use  'upload text file ’ option which can be accessed from the intermediary page described in     step 2. The text file can contain the mRNA names.  In the text file, each mRNA should be in new line,  
  9. Select servers from which you want the pre-computed lists of miRNAs targeting that gene (transcript), by clicking each or by using the selection     tool (Select at least one server for individual server prediction and select a minimum of two servers for ‘Comprehensive’ and ‘Shared targets’     Prediction),  
  10.  After you submit the selection, you will be directed to a page showing the links to detailed results. You can either view (in an html page) or        download the predictions from each individual server by clicking on the right option,  
  11. The comprehensive list gives you the non-redundant list of miRNAs that target your mRNA/s, collected from the servers selected by the user,  
  12. The shared miRNAs list, gives you only those miRNAs targeting the transcript/s that are common across the servers selected. This can be viewed        as a high confidence list because of the consensus predictions from multiple servers.  
     

How to map miRNAs to corresponding targets given two lists of miRNAs and mRNAs:

  
  1. To initiate the search, first click the ‘TarMiR tool’ link at the upper-right corner to bring up an intermediary page,  
  2. This page gives you two options, one for entering or pasting a list of miRNAs and/or mRNAs (recommended for small lists with less than 10 objects)      and the other one for uploading longer lists of miRNAs and/or mRNAs. Make your selection by clicking the appropriate link,  
  3. Select ‘Mapping miRNA- mRNA lists’ from the select prediction type drop-down menu,  
  4. Select species as Homo sapiens (for instance!),  
  5. Enter ‘Percentage cut-off’, i.e. the top “x” % ranked predictions from each server that you want to retrieve. Leaving the field blank will cause     TarMiR 1.0 to use the default value of 100%,  
  6. Enter or paste the miRNA name/s or miRBase accession number/s in the “Input one or more miRNAs” text box. Enter or paste the mRNA symbol     (gene symbol) in the “Input one or more mRNAs” text box. Since the species has already been selected, entering the species identifier (hsa) is     optional. When entering multiple miRNAs and mRNAs, make sure that each line contains only one entry,  
  7. Alternatively if your list of miRNAs and mRNAs is large, you can use ‘upload text file’ option which can be accessed from the intermediary page     described in step 2. The text file can contain the miRNA names and mRNA/gene symbols.  Use separate files for miRNAs and gene symbols and     upload them separately against the corresponding option,  
  8. Select servers from which you want the pre-computed lists of targets, by clicking each or by using the selection tool (Select at least one server for     individual server prediction and select a minimum of two servers for ‘Comprehensive’ and ‘Shared targets’ Prediction,  
  9. After you submit the selection, you will be directed to a page showing the links to detailed results. You can either view (in an html page) or     download the predictions from each individual server by clicking on the right option,  
  11. The comprehensive list gives you the non-redundant list of miRNAs/mRNAs that target your mRNAs/mRNAs, collected from the servers selected by     the user,  
  12. The shared targets list, gives you only those targets for the miRNA that are common across the servers selected. This can be viewed as a high        confidence list because of the consensus predictions from multiple servers.  
   
   

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