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-6722-5p -1.000 1892.000 0.175
hsa-miR-6724-5p -1.000 1809.000 0.190
hsa-miR-6726-3p -1.000 1035.000 0.420
hsa-miR-6726-5p -1.000 1776.000 0.195
hsa-miR-6727-3p -1.000 1419.000 0.289
hsa-miR-6727-5p -1.000 1801.000 0.190
hsa-miR-6728-3p -1.000 1420.000 0.289
hsa-miR-6728-5p -1.000 1938.000 0.168
hsa-miR-6729-3p -1.000 1421.000 0.289
hsa-miR-6729-5p -1.000 1376.000 0.299
hsa-miR-6730-3p 1.000 715.000 0.568
hsa-miR-6730-5p -1.000 1128.000 0.393
hsa-miR-6731-3p -1.000 1057.000 0.419
hsa-miR-6731-5p -1.000 1852.000 0.184
hsa-miR-6732-3p -1.000 1491.000 0.273
hsa-miR-6732-5p -1.000 2239.000 0.109
hsa-miR-6733-3p -1.000 877.000 0.494
hsa-miR-6733-5p -1.000 2047.000 0.147
hsa-miR-6734-3p -1.000 1058.000 0.419
hsa-miR-6734-5p -1.000 1895.000 0.174
hsa-miR-6735-3p -1.000 966.000 0.447
hsa-miR-6735-5p -1.000 2424.000 0.077
hsa-miR-6736-3p -1.000 1422.000 0.289
hsa-miR-6736-5p -1.000 1534.000 0.261
hsa-miR-6737-3p 1.000 468.000 0.683
hsa-miR-6737-5p -1.000 1382.000 0.296
hsa-miR-6738-3p -1.000 1059.000 0.419
hsa-miR-6738-5p -1.000 2632.000 0.038
hsa-miR-6739-3p 1.000 80.000 0.879
hsa-miR-6739-5p -1.000 2597.000 0.050
hsa-miR-6740-3p -1.000 1044.000 0.419
hsa-miR-6740-5p 1.000 766.000 0.543
hsa-miR-6741-3p -1.000 1292.000 0.335
hsa-miR-6741-5p -1.000 1945.000 0.167
hsa-miR-6742-3p 1.000 404.000 0.709
hsa-miR-6742-5p 1.000 516.000 0.659
hsa-miR-6743-3p -1.000 1060.000 0.419
hsa-miR-6743-5p -1.000 2427.000 0.076
hsa-miR-6744-3p -1.000 1233.000 0.356
hsa-miR-6744-5p -1.000 1677.000 0.225
hsa-miR-6745 -1.000 1790.000 0.192
hsa-miR-6746-3p 1.000 702.000 0.572
hsa-miR-6746-5p -1.000 2089.000 0.139
hsa-miR-6747-3p -1.000 1061.000 0.419
hsa-miR-6747-5p -1.000 2550.000 0.060
hsa-miR-6748-3p -1.000 1036.000 0.420
hsa-miR-6748-5p -1.000 2148.000 0.128
hsa-miR-6749-3p -1.000 1891.000 0.175
hsa-miR-6749-5p 1.000 797.000 0.529
hsa-miR-675-3p 1.000 700.000 0.572
hsa-miR-675-5p -1.000 2094.000 0.138
hsa-miR-6750-3p -1.000 2420.000 0.079
hsa-miR-6750-5p -1.000 2353.000 0.091
hsa-miR-6751-3p -1.000 870.000 0.500
hsa-miR-6751-5p 1.000 62.000 0.894
hsa-miR-6752-3p -1.000 1423.000 0.289
hsa-miR-6752-5p -1.000 1734.000 0.207
hsa-miR-6753-3p -1.000 1232.000 0.356
hsa-miR-6753-5p -1.000 1606.000 0.240
hsa-miR-6754-3p -1.000 1062.000 0.419
hsa-miR-6754-5p 1.000 684.000 0.583
hsa-miR-6755-3p 1.000 81.000 0.879
hsa-miR-6755-5p -1.000 1394.000 0.292
hsa-miR-6756-3p -1.000 1063.000 0.419
hsa-miR-6756-5p -1.000 1810.000 0.190
hsa-miR-6757-3p -1.000 1742.000 0.203
hsa-miR-6757-5p -1.000 1572.000 0.249
hsa-miR-6758-3p 1.000 469.000 0.683
hsa-miR-6758-5p -1.000 2474.000 0.071
hsa-miR-6759-3p 1.000 283.000 0.772
hsa-miR-6759-5p -1.000 1541.000 0.258
hsa-miR-676-3p 1.000 42.000 0.917
hsa-miR-676-5p -1.000 1020.000 0.427
hsa-miR-6760-3p 1.000 791.000 0.531
hsa-miR-6760-5p -1.000 2490.000 0.068
hsa-miR-6761-3p -1.000 1424.000 0.289
hsa-miR-6761-5p -1.000 1388.000 0.294
hsa-miR-6762-3p -1.000 894.000 0.485
hsa-miR-6762-5p -1.000 985.000 0.436
hsa-miR-6763-3p -1.000 1223.000 0.359
hsa-miR-6763-5p -1.000 1987.000 0.160
hsa-miR-6764-3p 1.000 388.000 0.713
hsa-miR-6764-5p 1.000 402.000 0.710
hsa-miR-6765-3p -1.000 1873.000 0.178
hsa-miR-6765-5p -1.000 1329.000 0.320
hsa-miR-6766-3p 1.000 97.000 0.870
hsa-miR-6766-5p -1.000 1654.000 0.230
hsa-miR-6767-3p 1.000 462.000 0.686
hsa-miR-6767-5p -1.000 2503.000 0.066
hsa-miR-6768-3p -1.000 1127.000 0.393
hsa-miR-6768-5p -1.000 2615.000 0.045
hsa-miR-6769a-3p -1.000 1425.000 0.289
hsa-miR-6769a-5p -1.000 1399.000 0.289
hsa-miR-6769b-3p -1.000 1040.000 0.420
hsa-miR-6769b-5p -1.000 2528.000 0.062
hsa-miR-6770-3p 1.000 755.000 0.551
hsa-miR-6770-5p -1.000 2251.000 0.107
hsa-miR-6771-3p -1.000 1492.000 0.273
hsa-miR-6771-5p -1.000 1996.000 0.157
hsa-miR-6772-3p 1.000 115.000 0.860
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