Freiburg RNA Tools
BrainDead - Results
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BrainDead 4526878

Input and runtime details for job 4526878 (precomputed example)

Training data

? Class-annotated RNAs in FASTA[.fa]

Model parameters

? k-mers of interest
AA,AGA,AGGU,AGU,AGUU,CU,GAA,GAGG,GG,GGG,GU,GUU,UGA,UGU,UU,UUG,UUGU,UUU
? k-mer features reflect
number of occurrences (feature is number >= 0)
? Max. energy ranked stable-3
? Machine learning model
Support Vector Classification using RBF kernel

Candidate data

? Candidate RNAs in FASTA[.fa]

Job ID 4526878 (server version trunk)

?Job Submitted & Queued@ Wed Feb 10 15:00:26 CET 2021
?BrainDead Started@ Wed Feb 10 15:16:53 CET 2021
?BrainDead Finished & Post-Processing@ Wed Feb 10 15:16:53 CET 2021
?Post-Processing Finished@ Wed Feb 10 15:17:07 CET 2021
?Job Completed@ Wed Feb 10 15:17:11 CET 2021
 DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4526878&toolName=BrainDead ( 30 days expiry )

Description of the job

miRNAs as ligands for microglia activation

This example summarizes our study that investigates the ability of mature miRNAs to act as immune receptor ligands. The ability of extracellular miRNAs to directly activate receptors is a recently discovered new field of operation of miRNAs beside their classic role in post-transcriptional gene regulation. The small RNAs available within the example's training data were experimentally tested for their potential to activate murine microglia cells in vitro. They are pre-classified as +/-1 when found activating or non-activating, resp., using fold change analyses based TNF-alpha concentration measurements. The example's training data set comprises both the original training data (top group) as well as the experimentally verified candidate sequences (middle and bottom group) from our initial BrainDead main publication (see list of references within Help page). For details on the selected k-mers, please refer to the manuscript. The candidate set covers all mature human miRNAs from mirBase v22.1.

? Output download complete results [zip]

Downloads

Predictions for candidate RNAs

Predicted class

Sort by selecting a column name.
RNA id class rank prob(1)
hsa-miR-586 1.000 185.000 0.820
hsa-miR-587 1.000 571.000 0.645
hsa-miR-588 -1.000 1212.000 0.364
hsa-miR-589-3p -1.000 2154.000 0.126
hsa-miR-589-5p -1.000 2258.000 0.106
hsa-miR-590-3p -1.000 1096.000 0.407
hsa-miR-590-5p -1.000 1692.000 0.220
hsa-miR-591 1.000 550.000 0.648
hsa-miR-592 1.000 394.000 0.713
hsa-miR-593-3p 1.000 59.000 0.895
hsa-miR-593-5p -1.000 1398.000 0.289
hsa-miR-595 -1.000 2370.000 0.087
hsa-miR-596 -1.000 1741.000 0.203
hsa-miR-597-3p 1.000 202.000 0.813
hsa-miR-597-5p 1.000 553.000 0.648
hsa-miR-598-3p 1.000 281.000 0.772
hsa-miR-598-5p 1.000 566.000 0.646
hsa-miR-599 1.000 53.000 0.899
hsa-miR-600 -1.000 1324.000 0.320
hsa-miR-601 1.000 161.000 0.833
hsa-miR-602 -1.000 1748.000 0.200
hsa-miR-603 1.000 543.000 0.648
hsa-miR-604 -1.000 2593.000 0.051
hsa-miR-605-3p -1.000 1448.000 0.284
hsa-miR-605-5p -1.000 2400.000 0.083
hsa-miR-606 -1.000 2359.000 0.089
hsa-miR-6068 -1.000 2230.000 0.110
hsa-miR-6069 -1.000 1754.000 0.200
hsa-miR-607 -1.000 1199.000 0.369
hsa-miR-6070 -1.000 1105.000 0.402
hsa-miR-6071 -1.000 2302.000 0.098
hsa-miR-6072 -1.000 1052.000 0.419
hsa-miR-6073 1.000 342.000 0.741
hsa-miR-6074 -1.000 1462.000 0.282
hsa-miR-6075 -1.000 1385.000 0.295
hsa-miR-6076 -1.000 1705.000 0.216
hsa-miR-6077 -1.000 1747.000 0.200
hsa-miR-6078 1.000 465.000 0.684
hsa-miR-6079 -1.000 1722.000 0.211
hsa-miR-608 1.000 445.000 0.693
hsa-miR-6080 1.000 377.000 0.721
hsa-miR-6081 -1.000 2216.000 0.113
hsa-miR-6082 -1.000 984.000 0.436
hsa-miR-6083 -1.000 1565.000 0.250
hsa-miR-6084 -1.000 1641.000 0.234
hsa-miR-6085 -1.000 2036.000 0.149
hsa-miR-6086 -1.000 1614.000 0.239
hsa-miR-6088 -1.000 2497.000 0.067
hsa-miR-6089 -1.000 2018.000 0.152
hsa-miR-609 1.000 732.000 0.557
hsa-miR-6090 -1.000 2100.000 0.137
hsa-miR-610 -1.000 1679.000 0.224
hsa-miR-611 -1.000 1374.000 0.300
hsa-miR-612 -1.000 1295.000 0.334
hsa-miR-6124 -1.000 2415.000 0.080
hsa-miR-6125 -1.000 2509.000 0.065
hsa-miR-6126 -1.000 2482.000 0.070
hsa-miR-6127 -1.000 1826.000 0.187
hsa-miR-6128 -1.000 1346.000 0.314
hsa-miR-6129 1.000 570.000 0.645
hsa-miR-613 1.000 440.000 0.695
hsa-miR-6130 1.000 756.000 0.551
hsa-miR-6131 -1.000 2508.000 0.066
hsa-miR-6132 -1.000 1984.000 0.160
hsa-miR-6133 1.000 776.000 0.536
hsa-miR-6134 -1.000 1442.000 0.285
hsa-miR-614 1.000 741.000 0.554
hsa-miR-615-3p -1.000 2262.000 0.105
hsa-miR-615-5p -1.000 1859.000 0.182
hsa-miR-616-3p 1.000 593.000 0.631
hsa-miR-616-5p -1.000 1643.000 0.234
hsa-miR-6165 -1.000 1436.000 0.287
hsa-miR-617 -1.000 980.000 0.439
hsa-miR-618 1.000 221.000 0.801
hsa-miR-619-3p 1.000 168.000 0.825
hsa-miR-619-5p -1.000 933.000 0.463
hsa-miR-620 -1.000 2598.000 0.050
hsa-miR-621 -1.000 1535.000 0.261
hsa-miR-622 1.000 174.000 0.822
hsa-miR-623 1.000 341.000 0.741
hsa-miR-624-3p -1.000 1294.000 0.334
hsa-miR-624-5p 1.000 254.000 0.784
hsa-miR-625-3p -1.000 1595.000 0.245
hsa-miR-625-5p -1.000 1816.000 0.189
hsa-miR-626 -1.000 1361.000 0.308
hsa-miR-627-3p 1.000 366.000 0.730
hsa-miR-627-5p -1.000 2417.000 0.080
hsa-miR-628-3p -1.000 2579.000 0.056
hsa-miR-628-5p 1.000 490.000 0.669
hsa-miR-629-3p 1.000 735.000 0.556
hsa-miR-629-5p -1.000 1254.000 0.349
hsa-miR-630 -1.000 1512.000 0.268
hsa-miR-631 -1.000 2102.000 0.136
hsa-miR-632 -1.000 1321.000 0.320
hsa-miR-633 -1.000 1953.000 0.166
hsa-miR-634 1.000 818.000 0.517
hsa-miR-635 1.000 739.000 0.554
hsa-miR-636 1.000 664.000 0.596
hsa-miR-637 -1.000 1309.000 0.329
hsa-miR-638 -1.000 1805.000 0.190
Rows: 1-100 101-200 201-300 301-400 401-500 501-600 601-700 701-800 801-900 901-1000 1001-1100 1101-1200 1201-1300 1301-1400 1401-1500 1501-1600 1601-1700 1701-1800 1801-1900 1901-2000 2001-2100 2101-2200 2201-2300 2301-2400 2401-2500 2501-2600 2601-2656 all

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When using BrainDead please cite :

Results are computed with BrainDead version 1.0.1 using IntaRNA 3.1.5 and Vienna RNA package 2.4.14