multiMiR
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KechrisLab
TargetScan Prediction Score cutoff interpretation
Hi,
I am trying to derive predicted targets for specific miRNAs. When looking at the targetScan results derived from the multiMir tools in comparision to the one derived from the targetScan website directly, I can not reproduce the results. Could you clarify how the cutoff for the prediction score is derived and how the ranking is done?
Here is the code and results. multiMir v1.20.0
mir <- "mmu-miR-322-3p
predCutoff <- 70
get_multimir(mirna = mir, table = "predicted", org = "mmu", predicted.cutoff = predCutoff)
database mature_mirna_acc mature_mirna_id target_symbol target_entrez target_ensembl score type 1 targetscan MIMAT0000549 mmu-miR-322-3p Abi3bp 320712 ENSMUSG00000035258 -0.137 predicted 2 targetscan MIMAT0000549 mmu-miR-322-3p Rhoa 11848 ENSMUSG00000007815 -0.155 predicted 3 targetscan MIMAT0000549 mmu-miR-322-3p Ipo7 233726 ENSMUSG00000066232 -0.167 predicted 4 targetscan MIMAT0000549 mmu-miR-322-3p Pik3ca 18706 ENSMUSG00000027665 -0.168 predicted 5 targetscan MIMAT0000549 mmu-miR-322-3p Marcks 17118 ENSMUSG00000069662 -0.168 predicted 6 targetscan MIMAT0000549 mmu-miR-322-3p Elavl4 15572 ENSMUSG00000028546 -0.173 predicted 7 targetscan MIMAT0000549 mmu-miR-322-3p Ywhag 22628 ENSMUSG00000051391 -0.184 predicted 8 targetscan MIMAT0000549 mmu-miR-322-3p Fbxw7 50754 ENSMUSG00000028086 -0.21 predicted 9 targetscan MIMAT0000549 mmu-miR-322-3p Cpeb2 231207 ENSMUSG00000039782 -0.223 predicted 10 targetscan MIMAT0000549 mmu-miR-322-3p Sp3 20687 ENSMUSG00000027109 -0.224 predicted 11 targetscan MIMAT0000549 mmu-miR-322-3p Meis2 17536 ENSMUSG00000027210 -0.228 predicted 12 targetscan MIMAT0000549 mmu-miR-322-3p Tfap2b 21419 ENSMUSG00000025927 -0.237 predicted 13 targetscan MIMAT0000549 mmu-miR-322-3p Hnrnpdl 50926 ENSMUSG00000029328 -0.26 predicted 14 targetscan MIMAT0000549 mmu-miR-322-3p Gpc4 14735 ENSMUSG00000031119 -0.27 predicted 15 targetscan MIMAT0000549 mmu-miR-322-3p Kmt2e 69188 ENSMUSG00000029004 -0.274 predicted 16 targetscan MIMAT0000549 mmu-miR-322-3p Fgf13 14168 ENSMUSG00000031137 -0.277 predicted 17 targetscan MIMAT0000549 mmu-miR-322-3p Zfand4 67492 ENSMUSG00000042213 -0.288 predicted 18 targetscan MIMAT0000549 mmu-miR-322-3p Map2k4 26398 ENSMUSG00000033352 -0.291 predicted 19 targetscan MIMAT0000549 mmu-miR-322-3p Smap1 98366 ENSMUSG00000026155 -0.309 predicted 20 targetscan MIMAT0000549 mmu-miR-322-3p Ube2v2 70620 ENSMUSG00000022674 -0.31 predicted 21 targetscan MIMAT0000549 mmu-miR-322-3p Paip2 67869 ENSMUSG00000037058 -0.405 predicted 22 targetscan MIMAT0000549 mmu-miR-322-3p Nfyb 18045 ENSMUSG00000020248 -0.411 predicted
The scores are comparable for most of the targets but the ranks clearly differ (Cumulative weighted context++ score).
TargetScan7 - https://www.targetscan.org/cgi-bin/targetscan/mmu_71/targetscan.cgi?mirg=mmu-miR-322-3p filtered results only showing the targets predicted by multiMir
| rank | Target gene | Representative transcript | Representative miRNA | Cumulative weighted context++ score | Total context++ score |
|---|---|---|---|---|---|
| 179 | Nfyb | ENSMUST00000130911.2 | mmu-miR-322-3p | -0.38 | -0.41 |
| 214 | Ube2v2 | ENSMUST00000115777.4 | mmu-miR-322-3p | -0.35 | -0.52 |
| 237 | Map2k4 | ENSMUST00000046963.4 | mmu-miR-322-3p | -0.34 | -0.35 |
| 331 | Smap1 | ENSMUST00000027339.8 | mmu-miR-322-3p | -0.28 | -0.31 |
| 334 | Fgf13 | ENSMUST00000033473.6 | mmu-miR-322-3p | -0.28 | -0.3 |
| 373 | Cpeb2 | ENSMUST00000169035.2 | mmu-miR-322-3p | -0.27 | -0.27 |
| 382 | Kmt2e | ENSMUST00000094962.3 | mmu-miR-322-3p | -0.26 | -0.3 |
| 385 | Hnrnpdl | ENSMUST00000128187.2 | mmu-miR-322-3p | -0.26 | -0.28 |
| 388 | Sp3 | ENSMUST00000102689.4 | mmu-miR-322-3p | -0.26 | -0.27 |
| 447 | Zfand4 | ENSMUST00000036503.8 | mmu-miR-322-3p | -0.24 | -0.3 |
| 448 | Meis2 | ENSMUST00000110907.2 | mmu-miR-322-3p | -0.24 | -0.29 |
| 703 | Pik3ca | ENSMUST00000029201.8 | mmu-miR-322-3p | -0.19 | -0.2 |
| 757 | Elavl4 | ENSMUST00000106598.2 | mmu-miR-322-3p | -0.18 | -0.24 |
| 830 | Ipo7 | ENSMUST00000084731.3 | mmu-miR-322-3p | -0.17 | -0.19 |
| 876 | Marcks | ENSMUST00000092584.5 | mmu-miR-322-3p | -0.17 | -0.17 |
| 917 | Ywhag | ENSMUST00000055808.5 | mmu-miR-322-3p | -0.16 | -0.18 |
| 1061 | Gpc4 | ENSMUST00000033450.2 | mmu-miR-322-3p | -0.14 | -0.32 |
| 1086 | Rhoa | ENSMUST00000007959.8 | mmu-miR-322-3p | -0.14 | -0.15 |
| 1750 | Paip2 | ENSMUST00000041314.9 | mmu-miR-322-3p | -0.08 | -1.07 |
| 2454 | Tfap2b | ENSMUST00000027059.5 | mmu-miR-322-3p | -0.04 | -0.24 |
| 3879 | Fbxw7 | ENSMUST00000107679.2 | mmu-miR-322-3p | 0 | -0.21 |
| 3953 | Abi3bp | ENSMUST00000048471.8 | mmu-miR-322-3p | 0 | -0.14 |
