Agarwal et al.

TargetScan Frequently Asked Questions (FAQs)

Web site

  1. What are the definitions of "conserved miRNA families","nonconserved miRNA families","conserved miRNA sites" and "nonconserved miRNA sites"?

  2. What do you mean by "Representative miRNA", "Aggregate PCT", or some other TargetScan term?

  3. If a gene has multiple transcripts, how can I know which one was used for target prediction?
  4. I study mouse genetics. Should I use mouse predictions from TargetScanHuman or TargetScanMouse? How do they differ?

  5. Sometimes the 3' UTR of my favorite genes don't match those I see in databases like NCBI RefSeq. As an example, mouse CD47 has a UTR length of about 4000 in TargetScanHuman, while NCBI RefSeq indicates a 3'UTR of about 800. Also, the mouse sequence in TargetScanHuman (NM_001025079) looks like it's actually a human sequence. Which annotation can I trust?

  6. How can I best predict miRNA site effectiveness? Should I look at site conservation or context score or something else?

  7. How can I download or export miRNA target predictions from TargetScan?

  8. How many unique genes are scanned by TargetScan?

  9. What are non-canonical sites?

  10. How are 'star' miRNAs (such as hsa-let-7b*) included in the compilation of miRNA families?
  11. What is the relationship between miRBase miRNAs and families and those in TargetScan? Are they identical?
  12. In TargetScan 5 Custom, nonconserved target sites are not shown; however, this information is available for annotated miRNAs. Is there a reason for this? Does TargetScan also predict nonconserved sites for all potential seed sequences?
  13. Where can I get more information about ...

  14. I would like to include results from a TargetScan analysis in a paper we are about to submit. Can I use these data in my publication? How should I cite TargetScan? Are there copyright concerns?
  15. Why doesn't TargetScan include predictions of miRNA regulation of long non-coding RNAs (lncRNAs)?

Data download

  1. I'd like to download and use all predicted TargetScan targets for my project, but I'd like to limit the dataset to high-confidence sites. What thresholds for Pct or context score should I use?
  2. What is meant by "Species ID" in the download tables?

  3. What do the numbers 1, 2, 3, etc. stand for in the "Site type" column of several tables?

  4. In the "Family Conservation" column of the miR Family table, what do the numbers refer to?
  5. I used BLAST to locate the TargetScan human 3' UTRs in the human genome. However, many of them didn't have perfect matches. Can you explain this?

  6. The download files, such as those for TargetScanHuman Release 6.1 appear to contain data that is different from the web site. How can I recover the same prediction results present in the web pages?

  7. How do you indicate start and end positions of predicted miRNA sites in the Data Download files? Are these influenced by genomic position or gaps in the alignment? How do you account for introns within a 3' UTR?
  8. We would like to download the TargetScan database. Is it possible to obtain the schema of the database so we can better understand the design?

TargetScan code

  1. I am interested in using TargetScan on a wide set of data. Is it possible to run batch queries or download the code and run the program locally?

  2. Do I need to use UTRs from multiple species for miRNA target prediction?