Integrating Diverse miRNA Target Prediction Datasets

The target predictions of PicTar [22 (link)] were downloaded from the UCSC database using the Table Browser and were migrated from hg17 to hg18 by applying the UCSC command line tool liftover. We used the predictions conserved in human, mouse, rat, chimp and dog (4-way) as well as the predictions additionally conserved in chicken (5-way). For fly we downloaded the sensitive prediction set (S1) of PicTar that is composed of predictions conserved in D. melanogaster, D. yakuba, D. ananassae, and D. Pseudoobscura, also via the UCSC Table Browser. Predictions for the human genome made by miRanda [6 (link)], release September 2008, were downloaded from http://microRNA.org[29 (link)]. Only predictions for transcripts contained in the RefSeq database were considered. Human and fly predictions made by miRBase Targets [7 (link)], version 5, were downloaded from http://microrna.sanger.ac.uk/targets/v5/. RNA22 [23 (link)] predictions for human 3'UTR sequences were downloaded from http://cbcsrv.watson.ibm.com/rna22.html. Since these predictions were made using Ensembl transcripts, we mapped the predictions to RefSeq genes by applying mapping tables provided by Ensembl and UCSC. Predictions of PITA [9 (link)] were downloaded from http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html. We utilized the "TOP" and the "ALL" set with 3/15 flankings. TargetScanS [13 (link)] predictions and the corresponding microRNA family mapping table were downloaded from http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_50. Predictions made by Gaidatzis et al. [20 (link)] were downloaded from the EIMMo server http://www.mirz.unibas.ch/. Targets predicted by mirTarget2 (version 3) [21 (link)] were downloaded from http://mirdb.org/miRDB. Human target site predictions of DIANA-microT v3.0 [30 (link)] were retrieved via the web server at http://diana.cslab.ece.ntua.gr/microT/ for the thresholds loose (score = 7.3) and strict (score = 19). Finally, we downloaded the human target site predictions of TargetRank [26 ] from http://hollywood.mit.edu/targetrank/.

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Sturm M., Hackenberg M., Langenberger D, & Frishman D. (2010). TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics, 11, 292.

Publication 2010

3'utr Chicken Chimp Genes Genie Human Human genome Microrna Mouse Pubs Vert

Corresponding Organization :

Other organizations : Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Universidad de Granada, Leipzig University, Weihenstephan-Triesdorf University of Applied Sciences, Technical University of Munich

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Protocol cited in 22 other protocols

Variable analysis

independent variables

The target predictions of PicTar were downloaded from the UCSC database using the Table Browser and were migrated from hg17 to hg18 by applying the UCSC command line tool liftover.
Predictions for the human genome made by miRanda, release September 2008, were downloaded from http://microRNA.org.
Human and fly predictions made by miRBase Targets, version 5, were downloaded from http://microrna.sanger.ac.uk/targets/v5/.
RNA22 predictions for human 3'UTR sequences were downloaded from http://cbcsrv.watson.ibm.com/rna22.html.
Predictions of PITA were downloaded from http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html.
TargetScanS predictions and the corresponding microRNA family mapping table were downloaded from http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_50.
Predictions made by Gaidatzis et al. were downloaded from the EIMMo server http://www.mirz.unibas.ch/.
Targets predicted by mirTarget2 (version 3) were downloaded from http://mirdb.org/miRDB.
Human target site predictions of DIANA-microT v3.0 were retrieved via the web server at http://diana.cslab.ece.ntua.gr/microT/.
The human target site predictions of TargetRank were downloaded from http://hollywood.mit.edu/targetrank/

dependent variables

The target predictions of PicTar for human, mouse, rat, chimp and dog (4-way) as well as the predictions additionally conserved in chicken (5-way).
The sensitive prediction set (S1) of PicTar for fly that is composed of predictions conserved in D. melanogaster, D. yakuba, D. ananassae, and D. Pseudoobscura.

control variables

Predictions for transcripts contained in the RefSeq database were considered for miRanda, miRBase Targets, and RNA22.
The predictions of PITA were utilized from the "TOP" and the "ALL" set with 3/15 flankings.

Annotations

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